diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..177e5aa
--- /dev/null
+++ b/NEWS
@@ -0,0 +1,3655 @@
+
+
+
+BoutrosLab.plotting.general 7.1.2 2024-09-06
+
+UPDATE
+* Improved "sample.order" argument checking
+* Cleaned the C++ namespace by using `R_` versions of Free, Calloc, and Realloc
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.1.1 2024-01-08
+
+UPDATE
+* Improved documentation for type parameter in create.scatterplot
+* Fix typo in README
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.1.0 2023-10-26
+
+ADDED
+* Add testthat framework for package tests
+* Use mockr for unit testing
+* Improve documentation for automatic axis scaling in:
+  - create.scatterplot
+  - create.boxplot
+  - create.manhattanplot
+  - create.hexbinplot
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.10 2023-10-09
+
+UPDATE
+* Add deprecation warning for test file in preparation for using
+  testthat in the v8.0.0 release
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.9 2023-07-21
+
+UPDATE
+* Run R CMD check GitHub action weekly and with manual dispatch
+* Updated GitHub links to use new "package" prefix
+
+REMOVED
+* Remove unnecessary package manual file
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.8 2023-05-26
+
+UPDATE
+* Change name of print.to.file() to export.to.file() to avoid naming conflict
+  with S3 method print()
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.7 2023-05-25
+
+UPDATE
+* Expose panel.text arguments for text.above.bar options in create.barplot
+* Remove duplicated code in print.multipanel
+* Update format of CRAN links
+
+BUG
+* Add default label locations for continuous legends
+* Fix error with expressions in main for multipanelplots
+
+REMOVED
+* Remove outdated plotting data storage code
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.6 2023-02-15
+
+UPDATE
+* Move CICD workflow from Dockerhub to GitHub packages
+* Add github PR template
+
+UPDATE
+* Add text support for create.histogram
+
+UPDATE
+* Remove axis labels with axis.lab = NULL in create.boxplot for consistent behavior with other plot types
+
+BUG
+* Fix ylab.axis.padding parameter in create.histogram
+* Fix error when using expressions in multipanelplot labels and main
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.5 2023-01-03
+
+UPDATE
+* Fix typo in man/create.violinplot.Rd
+* Add alpha parameter to create.boxplot
+* Added GitHub repo to package description
+* Correctly sort horizontal barplot
+* Remove Makefile
+* Replaced string class comparison with is()
+
+BUG
+* Fix NEWS format
+* Fix bug with persisted plotting function output in examples
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.4 2022-08-17
+
+UPDATE
+* Fix border specification in create.polygonplot
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.3 2022-03-15
+
+UPDATE
+* Update .Rbuildignore to match lab R standards
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.2 2022-03-07
+
+BUG
+* Add type comparisons for class name comparisons
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.1 2022-03-03
+
+BUG
+* Fix object protection issue in distance.c
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 7.0.0 2022-02-15
+
+UPDATE
+* Renamed ks.test.critical.value() function to critical.value.ks.test()
+  to resolve naming conflict with S3 generic ks.test() from base R stats
+  package.
+
+BUG
+* Fix issue when specifying multiple line-widths in create.polygonplot()
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 6.1.0 2021-10-26
+
+UPDATE
+* Add option to use dots in a legend instead of default rectangles
+* Enable create.boxplot to print different text label on each panel
+
+BUG
+* Fixed inconsistent grouping of point colours in create.boxplot
+* Account for case where only one colour is passed to create.heatmap
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 6.0.3 2021-01-24
+
+UPDATE
+* Only use cairo in the examples for covariates.grob and legend.grob
+  if capabilities('cairo') is true.
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 6.0.2 2021-01-04
+
+UPDATE
+* Depends versions: R (>= 3.5.0), lattice (>= 0.20-35),
+  latticeExtra (>= 0.6-27), cluster (>= 2.0.0), hexbin (>= 1.27.0)
+* Only use cairo when capabilities('cairo') is true to fix CRAN's issue
+  of cairo not being available on M1 Macs
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 6.0.1 2020-08-05
+
+UPDATE
+* Added paper's doi to DESCRIPTION
+
+REMOVED
+* Removed use of tocstyle package in PlottingGuide as that is obsolete
+  and failing CRAN's check
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 6.0.0 2020-04-01
+
+UPDATE
+* Updated contact email
+* Included source code previously imported from BoutrosLab.dist.overload
+  and BoutrosLab.statistics.general
+* Fixed resolutions for examples to reduce running time
+* Added \donttest{} to examples that took >5 seconds to run
+* Examples now output plots to tempdir()
+
+BUG
+* Fixed errors in create.multiplot and create.multipanel that wasn't
+  passing CRAN's check by changing 'is.na' to 'anyNA'
+* Fixed errors in create.multiplot that was only checking the first
+  element in a list by using 'is.element' instead of '=='
+* Fixed spacing issue in PlottingGuide
+* Added stringsAsFactors = TRUE to data.frame() calls in examples
+  (Changes to R-devel in 2020-03-04 changed the defaults)
+* Fixed thousands.splits to return a vector instead of a list
+* Fixed write.metadata to use double quotes on system calls, correctly
+  show BL.plotting.survival version and consolidate exiftool calls
+  to speed things up
+* Fixed CRAN error misuse of package= for PACKAGE=
+
+REMOVED
+* Removed BoutrosLab.utilities::recode.vector calls in examples
+* Removed requirements for BoutrosLab.utilities, BoutrosLab.dist.overload,
+  BoutrosLab.statistics.general
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.9.8 2018-10-16
+
+FEATURE
+* create.hexbinplot: added option to modify the default legend title
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.9.7 2018-09-19
+
+BUG
+* fixed an issue regarding warning detection for class of conditioning variable that didn't recognize character input (barplot, boxplot, hexbinplot, scatterplot)
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.9.6 2018-07-24
+
+BUG
+* fixed an issue that prevented extra points from plotting correctly in create.polygonplot
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.9.5 2018-06-05
+
+FEATURE
+* added warnings when a formula contains a conditioning variable that is an integer/numeric (barplot, boxplot, hexbinplot, scatterplot)
+* changed default xaxis.tck for boxplot to prevent automatic ticks from appearing at top of plot
+
+BUG
+* force.colour.scheme no longer requires 'x' when return.scheme = TRUE
+* fixed an error in create.scatterplot preventing automatic axis determination when all y == 0 or all y == -N
+
+REMOVED
+* removed append.footnote.R as it was non-functional with no plans to fix
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.9.4 2018-04-18
+
+FEATURE
+* dotmap can now do symmetrical removing of top left half of dotmap
+
+BUG
+* top covariates in heatmap now have proper defaults
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.9.3 2018-04-18
+
+FEATURE
+* updated dependencies to not include as many
+* boxplot now saves all its data (for later use)
+* multipanelplot now saves temp plots to temp dir
+
+BUG
+* Default.colours no longer references wrong grey scale colour
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.9.2 2018-04-10
+
+FEATURE
+* Legend grob for continous legends now auto place themselves -- x and y pos dont do anything anymore
+* Print to file will now override previous entries
+* removed printing for individual plot info (too unreliable)
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.9.1 2018-04-04
+
+FEATURE
+* Multipanel plot now uses tob axis labels too for lining up plots
+
+BUG
+* Multipanel plot now correctly positions plot main labels
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.9.0 2018-03-23
+
+FEATURE
+* added code for saving data information and trellis object information to each relevant plot
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.16 2018-03-16
+
+FEATURE
+* cleaned up the multipanelplot code and updated the examples
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.15 2018-03-13
+
+FEATURE
+* made multipanelplot legend/label placement algorithm more optimal
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.14 2018-03-09
+
+FEATURE
+* now stores data on the mount
+
+BUG
+* text now passed to panel in seperate list, stopping it from being reset in between plots
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.13 2018-02-13
+
+FEATURE
+* adjusted polygon plot to work well with roc plot
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.12 2018-02-08
+
+FEATURE
+* added lollipop plot as an extension of scatterplot
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.11 2018-02-05
+
+FEATURE
+* added ability to disable factor sorting in relative plots
+* added example to histogram of type change
+
+
+BoutrosLab.plotting.general 5.8.10 2018-01-22
+
+FEATURE
+* added border colour for histogram bars
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.9 2018-01-12
+
+FEATURE
+* added inside legend auto finder code
+
+BUG
+* boxplot addstriplot colour was having issue with multiple boxplots, now works properly
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.8 2017-12-19
+
+UPDATE
+* updated formatting to match coding standard
+* added inside legends to multipanel plot
+
+BUG
+* heatmap now accepts both x and y axis covariates
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.7 2017-11-15
+
+UPDATE
+* updated formatting to match coding standard
+
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.6 2017-11-15
+
+FEATURE
+* legend and covariate grobs can now use x and y coordinates
+
+BUG
+* heatmap using colours must faster
+* legacy settings in multipanel plot now affect all individual plots too
+
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.8.5 2017-11-01
+
+FEATURE
+* force colour scheme now has heteroplasmy fraction and MT annotation
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.4 2017-10-25
+
+BUG FIX
+* Multipanel plot now accepts colorkey and draw key legends
+* Get defaults now retrieves ArialMT instead of Arial font (actual name on Linux)
+
+FEATURE
+* heatmap can now use colours to specify the squares
+* density plot can now add text (like bar/boxplot)
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.3 2017-08-11
+
+BUG FIX
+* Multipanel plot now works with legends from original plots
+* Barplot error bars now work with horizontal plots too
+
+FEATURE
+* heatmap now accepts inside legends and can specify text not based on grid cooridnates
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.2 2017-08-11
+
+BUG FIX
+* Completely reworked how spacing works in multipanel plot -- now creates rectangular grobs instead of using top/left/right/bottom padding
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.1 2017-08-11
+
+BUG FIX
+* Multipanel plot background colour
+* Multipanel plot not accepting expression labels
+* Multipanel deleting plots main labels
+* heatmap legend layout works properly now
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.8.0 2017-08-11
+
+ADDITIONS
+* new create.multiplot function (create.multipanelplot)
+
+BUG FIX
+* auto-axis now gives 5 labels by default instead of 4
+* same.as.matrix can now be applied to create dendrogram outside of heatmap
+* fixed filename error in crete.gif
+* heatmap now loads defaults
+* segplot defaults to bold like rest of plots
+* colours for default dotmap now match the documentation (had to reverse them)
+
+FEATURE UPDATE
+*pcawg.colours: new and renamed tumour type names added to palette, sv class 'insertion' assigned colour
+
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.7.6 2017-08-11
+
+BUG FIX
+* 1D heatmaps now work -- automatically
+* Error bars now work properly with grouped bar plots
+
+FEATURES
+* automatic layout justification for legends (using just arg) for continous legends
+* added helper function for seperating thousands by commas, i.e -> (12345) -> (12,345)
+* merged all the relevent colour functions into force.colour.scheme
+* can now extract dendrograms from a heatmap (only one, and may require manual manipulation)
+
+
+
+--------------------------------------------------------------------------
+
+BUG FIX
+* create.heatmap - grid row/column limits reversed
+* legend.grob - continuous legends produce warnings
+* ytop.rectangle in create.scatterplot() doesn't work properly.
+* Remove the old option (retrieve.plot.labels) and merge into (plot.labels.to.retrieve)
+
+FEATURES
+* merged multiple colour functions (old ones to be removed in next commit)
+* multiple colours of error bars in scatterplot
+* Add xaxis.rot.top option to create.multiplot
+* have legends on both the left AND the right for create.heatmap
+
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.7.4 2017-07-19
+
+BUG FIX
+* Automatic labels not working for stacked barplots
+* removed log scaling from stacked barplots
+* fixed 1 D heatmap issues
+
+ADDITIONS
+* search metadata function
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.7.3 2017-06-06
+
+FEATURE UPDATE
+* each plot can put xat/yat = "auto"/"auto.linear"/"auto.log" to get automatic labels
+
+ADDITIONS
+* pretty axis function -- input data set gives updated data values and labels
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.7.2 2017-05-17
+
+FEATURE UPDATE
+* Can now add border to correlation keys
+* Issues around multiplot reseting labels on y axis when x asis labels added solved
+
+ADDITIONS
+* create.gif for creating animated plots
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.7.1 2017-05-17
+
+BUG FIX
+* write.plot.R: fixed an error that didn't allow adding additional plots when returning object to screen (when filename = NULL)
+* create.barplot.R: fixed a bug interfering with add.rectangle and removed redundant add.background.shading (repeats add.rectangle functionality)
+* force.colour.scheme: if multiple outputs were requested only one would be returned; now returns a list
+
+FEATURE UPDATE
+* create.barplot.R: minor improvements to some examples
+	*split argument lwd into axes.lwd and border.lwd to be consistent with other functions
+	*removed argument remove.all.border.lines as this can now be accomplished with axes.lwd
+
+MINOR (FORMATTING) CHANGES
+* colour.gradient.R, covariates.grob.R, create.barplot.R, create.boxplot.R, create.colourkey.R, create.dendrogram.R, create.densityplot.R,
+	create.hexbinplot.R, create.segplot.R, create.stripplot.R, create.violinplot.R, default.colours.R, display.colours.R,
+	display.statistical.result.R, force.colour.scheme.R, generate.at.final.R, get.corr.key.R, get.defaults.R, get.line.breaks.R, legend.grob.R,
+	scientific.notation.R, show.available.palettes.R, write.metadata.R, write.plot.R:
+	applied code formatting (BL standards)
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.7.0 2017-05-11
+
+BUG FIX
+* create.violinplot: fixed a bug in colour functionality; now repeats colours when fewer colours are supplied than there are groups
+
+FEATURE UPDATE
+* create.hexbinplot: changed argument abline.type to abline.lty to be consistent with other functions
+* create.segplot: added warning for specific use case (multiplot fails when a vertical segplot is the first plot)
+* create.manhattanplot: changed argument axis.lwd to axes.lwd to be consistent with other functions
+
+MINOR (FORMATTING) CHANGES
+* create.hexbinplot, create.histogram, create.manhattanplot, create.polygonplot, create.qqplot.comparison, create.qqplot.fit,
+	create.scatterplot, create.stripplot, create.segplot, create.violinplot, age.categorical.colour, append.footnote:
+	applied code formatting (BL standards)
+
+--------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.6.24 2017-04-20
+
+FEATURE UPDATE
+*create.multiplot: Added functionality to add top x-axis tick labels. Has not been extensively tested.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.23 2017-02-09
+
+BUG FIX
+*pcawg.colours: fixed bug that prevented project code colours from being returned.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.22 2017-02-09
+
+FEATURE UPDATE
+*create.dotmap: addition of parameters for rectangle border thickness, rectangle border colour.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.21 2017-01-30
+
+BUG FIX
+* create.scatterplot: adding conditional for when pch is not referring
+  to a point (this is in reference to KM plots)
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.20 2017-01-28
+
+FEATURE UPDATE
+* create.scatterplot: addition of parameter "col.border".
+  This allows customizable border colours when pch >= 21.
+
+--------------------------------------------------------------------------
+
+
+BoutrosLab.plotting.general 5.6.19 2016-12-06
+
+FEATURE UPDATE
+* pcawg.colours: add project.code to colour.schemes
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.18 2016-11-23
+
+FEATURE UPDATE
+* create.polygonplot: option to add rectangles.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.17 2016-11-08
+
+FEATURE UPDATE
+* pcawg.colours: consistent colour palette for use on pcawg data
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.15 2016-10-24
+
+FEATURE UPDATE
+* create.heatmap: rotation of the top x axis labels is now independent from the bottom x axsis labels.
+* create.multiplot: options to set the distance between tick marks and tick labels
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.14 2016-10-05
+
+FEATURE UPDATE
+* create.polygonplot: option to add text.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.13 2016-09-28
+
+FEATURE UPDATE
+* create.polygonplot: added parameters alpha and median.lwd.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.12 2016-09-07
+
+FEATURE UPDATE
+* create.densityplot & create.violinplot: allow adjustment of bandwidth with parameters bandwidth and bandwidth.adjust.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.11 2016-08-31
+
+FEATURE UPDATE
+* create.stripplot: allow different border colour for added points when pch >= 21
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.10 2016-07-27
+
+BUG FIX
+* reintegrated untagged changes to trunk and re-added scatterplot feature updates.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.9 2016-07-25
+
+FEATURE UPDATE
+* create.scatterplot: allow different border colour for added points when pch >= 21
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.8 2016-05-27
+
+FEATURE UPDATE
+* create.dotmap:
+	Added parameters 'columns' and 'rows' for spot.colour.function to allow dots colours to be grouped by columns or rows, respectively [BPG-16].
+	There are 12 distinct colours (the default colours) and the colours start to repeat when there are more than 12 columns/rows.
+	It also checks that the columns/rows (depending on which side is selected) are unique and throws and error if they are not.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.7 2016-05-19
+
+BUG FIX
+* create.multiplot: fixed bug where NULL values in parameter list (for xlimits=/ylimits=) were being ignored/unprocessed [BPG-2].
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.6 2016-04-29
+
+FEATURE UPDATE
+* create.barplot:
+	Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' to allow users to add text labels to plot area.
+	Added parameter 'box.ratio' for adjusting thickness of each bar.
+	Added parameter 'remove.all.border.lines' to allow barplots with no borders.
+	Added example for adding text to plot and adjusting box.ratio.
+
+BUG FIX
+* create.barplot: fixed adding error bars for data-frames [BPG-4]
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.5 2016-04-27
+
+MINOR UPDATE
+* create.boxplot: Added example for adding text to plot.
+* create.hexbinplot: Added example of stratified multiplot.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.4 2016-04-21
+
+FEATURE UPDATE
+* create.dotmap: NA plotting character can be made different colours with new variable, NA.spot.size.colour.
+	Default is set to black.
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.6.2 2016-04-08
+
+FEATURE UPDATE
+* get.cor.key: parameterizing number of decimal places to keep for spearman, pearson and kendall correlation values
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.4.3 2016-01-04
+
+BUG FIXES:
+* Inconsitency in dotmap/heatmap grid lines location fixed -> everything follows heatmaps spec now
+  fixed bug where sample.order would reorde barplots incorrectly when horizontal
+* default font sizes are consistent now
+* default font sizes are more proportional
+
+FEATURE UPDATES:
+* ability to add multiple violin fill colours
+* able to completely remove borders from heatmaps
+* add p values automatically to box plots
+* ability to set a sperate set of defaults based on type of publication ( default sets still need to be added)
+* ability to pick what plots to retrieve plot labels from in create.multiplot
+
+--------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.4.2 2015-12-22
+
+FEATURE UPDATE:
+* create.scatterplot: added option to specify colour of grid lines.
+
+-------------------------------------------------------------------------
+
+BoutrosLab.plotting.general 5.3.9 2015-10-01
+
+FEATURE UPDATE:
+* create.heatmap: turns off grid lines when row or column number exceeds a certain threshold.
+* auto-removal of grid lines can be overrided with forcing parameters
+
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.3.7
+
+BUG FIXES:
+* same.as.matrix will now correcting readjust label specifications
+* when combining scatterplots, they will no longer only use error bars from one scatter plot
+* yaxis.covariates parameter can now allow specific location specification so it does not overlap the heatmap
+* xgrid.at and ygrid.at now properly update for all functions
+* background rectangles are now drawn in the background instead of foreground
+* when combining scatterplots, they will no longer only use the text specified from one scatter plot
+* removed circular definitions from Rd files
+* standardized parameter defaults
+
+FEATURE UPDATES:
+* Can now add subtitles through use of xaxis.top parameters
+* Can now input a vector of files to be output to
+* Can now sort boxes in create.boxplot by max, min, mean and median (defaults to median if not set)
+* Can now draw both bands and lines on segplots
+* Polygon plot will now auto-calculate x and y limits if not specified
+* Can now vertically align labels and adjust there coordinates manually
+
+BoutrosLab.plotting.general 5.3.4 2015-07-31
+
+MINOR UPDATE:
+* create.scatterplot: updated ROC example to use auto-label placement
+
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.3.3 2015-07-28
+
+MINOR UPDATE:
+* functions containing the word 'colour' now accept both American and Canadian spelling
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.3.2 2015-07-24
+
+BUG FIXES:
+* create.heatmap: fixed bug which made labels disappear when stratifying dendrogram
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.3.1 2015-07-24
+
+MINOR UPDATE:
+* minor updates to the plotting guide
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.3.0 2015-07-23
+
+MINOR UPDATE:
+* standardized parameter names across all plotting functions
+* create.hexbinplot: added add.xyline and add.curves functionality (same as in create.scatterplot)
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.20 2015-07-13
+
+MINOR UPDATE:
+* create.barplot, create.boxplot, create.hexbinplot, create.manhattanplot, create.polygonplot, create.scatterplot, create.segplot, create.stripplot, create.violinplot: Set xlab.label and ylab.label to default to formula components
+* default.colours: greyscale check no longer runs if only one colour is requested
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.19 2015-07-03
+
+MINOR UPDATE:
+* force.colour.scheme: added snv colour scheme
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.18 2015-07-03
+
+MINOR UPDATE:
+* Standardized all plotting functions to have resolution set to 1600 dpi
+* force.colour.scheme: Added spaces in appropriate tissue names
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.17 2015-06-16
+
+MINOR UPDATE:
+* removed out-of-date comments from examples
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.16 2015-06-15
+
+MINOR UPDATE:
+* re-created PlottingGuide to use revamped show.available.palettes function
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.13 2015-05-08
+
+MINOR UPDATE
+* create.multiplot: added example showing how to save parameter options from individual plots
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.12 2015-05-07
+
+MINOR UPDATE
+* create.heatmap: Added two parameters: text.position and text.offset to customize placement of text in cells
+* show.available.palettes: changed display of specific schemes to call create.heatmap (more robust method)
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.10 2015-04-22
+
+BUG FIXES
+* show.available.palettes: fixed 'general' program to no longer introduces NAs by coersion
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.9 2015-04-21
+
+MINOR UPDATE
+* create.hexbinplot: added comment to explain maxcnt removing datapoints from example plot
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.8 2015-03-12
+
+MINOR UPDATE
+* create.barplot: allow vector of custom sorting order for samples
+* create.multiplot: has flag to remove all border lines from plots
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.6 2014-12-24
+
+MINOR UPDATE
+* write.plot: fixed bug
+* added new colourkey legend and interface
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.5 2014-12-18
+
+MINOR UPDATE
+* updated plotting guide to have more examples and slight wording adjustments
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.4 2014-12-16
+
+MINOR UPDATE
+* create.barplot: ablines now appear in the background of the plot instead of the foreground
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.2 2014-12-09
+
+MINOR UPDATE
+* write.plot: Added embed.plot functionality (depreciating said function)
+* embed.plot: Removed embed.plot()
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.1 2014-11-05
+
+MINOR UPDATE
+* force.colour.scheme: Bug fix for annovar colour schemes
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.2.0 2014-10-17
+
+MINOR UPDATE
+* Added `Nature' style option to all plotting functions
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.9 2014-10-16
+
+MINOR UPDATE
+* create.scatterplot: for add.line.segments, changed line-end style to 'butt'
+* create.stripplot: NEW ARGUMENTS to allow for addition of lines showing group medians
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.7 2014-10-10
+
+MINOR UPDATE
+* default.colours: added new schemes spiral.noon and spiral.night
+* default.colours: rearranged order of qual scheme to decrease red-green combinations
+* force.colour.scheme: changed CNV colours to red/blue/green/white, MSI to green/yellow, risk to red/yellow
+* reorganized default.colours and force.colour.scheme to return deprecated schemes
+* show.available.palettes: reorganized layout of 'specific' scheme output
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.6 2014-10-08
+
+MINOR UPDATE
+* create.boxplot: added arguments to allow for addition of stripplot in background
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.5 2014-09-19
+
+MINOR UPDATE
+* show.available.palettes: added new function to show schemes available in default.colours and
+force.colour.scheme
+* default.colours: refactored, changed greyscale warning to auto-calculate
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.4 2014-09-08
+
+MINOR UPDATE
+* create.scatterplot: changed argument name - add.lines > add.line.segments
+* create.scatterplot: updated to accept lists of line segments to add
+---------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.3 2014-08-22
+
+MINOR UPDATE
+* PlottingGuide: converting to use knitr, added further details and references to design portion
+* MultiPlotTutorial: deleted, contents migrated to PlottingGuide
+
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.2 2014-08-14
+
+MINOR UPDATE
+* create.manhattanplot: Updated documentation to use chromosome palette in force.colour.scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.1 2014-08-14
+
+MINOR UPDATE
+* create.barplot: changed default fill colour to black (instead of grey)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.1.0 2014-08-12
+
+MINOR UPDATE
+* create.scatterplot: NEW ARGUMENTS text.guess.* now allows users to specify data points so that
+  associated label positions can be automatically determined
+* inside.rectangle: NEW FUNCTION which determines if a set of data points are inside a set of defined
+  rectangles
+* inside.ellipse: NEW FUNCTION which determines if a set of data points are inside a set of defined
+  ellipses
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.28 2014-08-08
+
+MINOR UPDATE
+* Updated plotting guide to have extended design advice: added sections on resolution, file types, etc
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.27 2014-07-31
+
+MINOR UPDATE
+* Updated examples in scatterplot, qqplot comparison, hexbinplot, heatmap, dotmap, and barplot to have better formatted axes labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.26 2014-07-31
+
+BUG FIX
+* re-added argument line.lwd in create.scatterplot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.25 2014-07-31
+
+MINOR UPDATE
+* create.heatmap: NEW ARGUMENT gridline.order now allows user to specify in which order
+  gridlines should be drawn (horizontal or vertical first)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.24 2014-07-31
+
+MINOR UPDATE
+* adjusted examples in qqplot.comparison, qqplot.fit and scatterplot to use character values for panel groupings
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.23 2014-07-30
+
+MINOR UPDATE
+* display.colours now additionally displays names of colours
+
+BUG FIX
+* added 'eye' to the 'tissue' palette in force.colour.scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.22 2014-07-29
+
+MINOR UPDATE
+* Fixed: create.scatterplot, add.lines now works with lists of data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.20 2014-07-24
+
+MINOR UPDATE
+* Changed multiplot example to use matching gene data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.19 2014-07-23
+
+MINOR UPDATE
+* Changing chromosome palette in force.colour.scheme to use more visually distinct colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.18 2014-07-23
+
+BUG FIX
+* Changed datasets keep common genes among datasets
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.17 2014-07-21
+
+MINOR UPDATE
+* Updated multiplot tutorial with new examples using generate data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.16 2014-07-16
+
+BUG FIX
+* default.colours: properly return the requested number of colours when multiple palettes requested
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.15 2014-07-11
+
+MINOR UPDATE
+* create.scatterplot:
+	- NEW ARGUMENTs allow for addition of line segments to be drawn
+BUG FIX
+* get.corr.key: fixed corner definition determined by x.pos and y.pos
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.14 2014-07-07
+
+MINOR UPDATE
+* create.scatterplot:
+	- NEW ARGUMENT allows for specification of strip title fontface
+* create.stripplot:
+	- NEW ARGUMENT allows for specification of strip title fontface
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.11 2014-07-04
+
+MINOR UPDATE
+* added example to create.dotmap clustered by dots and dendrogram added
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.10 2014-07-04
+
+MINOR UPDATE
+* renamed colour schemes in default.colours to follow spiral.<timeofday> format
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.10 2014-07-04
+
+MINOR UPDATE
+* added biomolecule colour scheme to force.colour.schemes
+* migrated chromosome colour scheme to force.colour scheme from default.colours
+* renamed extra colour schemes in default.colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.9 2014-07-03
+
+MINOR UPDATE
+* formatting adjustments to examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.8 2014-07-03
+
+MINOR UPDATE
+* changed SNV dataset numerical coding to be simpler
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.7 2014-07-02
+
+BUG FIXES
+* palettes in default.colours function properly return subsets
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.6 2014-06-13
+
+MINOR UPDATE
+* force.colour.scheme now accepts both upper and lower case input
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.5 2014-06-11
+
+MINOR UPDATE
+* Changed default sequential, diverging, and binary schemes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.4 2014-06-10
+
+MINOR UPDATE
+* Added more schemes to default.colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.3 2014-06-04
+
+MINOR UPDATE
+* Added plotting guide to vignettes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.2 2014-06-02
+
+BUG FIXES
+* create.barplot:
+  - Re-added origin to panel call to allow for negative bars
+  - Set y-axis default values to appear automatically
+  - Fixed ordering of bars by increasing data
+* create.histogram: Silenced warning caused by data parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.1 2014-06-02
+
+MINOR UPDATE
+* force.colour.scheme: Added colour schemes in addition to the 'annovar' schemes
+* default.colours: Added additional 5-colour palette
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 5.0.0 2014-05-29
+
+MAJOR UPDATE
+* create.scatterplot.with.error: Removed function, merged with create.scatterplot
+* panel.BL.bwplot: Removed function, functionality no longer needed
+* create.multiple.stripplots: Removed function, functionality contained within create.stripplot
+* create.multiple.boxplots: Removed function, functionality contained within create.boxplot
+* create.barplot.with.error: Removed function, functionality contained within create.barplot
+* rgb.to.greyscale: Removed function, moved into display.colours
+* colour.to.grey: Removed function, moved into display.colours
+* scientific.notation.2: Removed function, functionality contained within scientific.notation
+* scientific.notation.expr: Removed function, functionality contained within scientific.notation
+* create.violinplot: Renamed function from create.violin.plot
+* create.polygonplot: Renamed function from create.polygon
+
+MINOR UPDATE
+* Code and documentation base reviewed to match lab formatting standard
+* Updating examples in documentation to use standard datasets instead of fake data
+* create.multiplot: Updated example plots to use standard dataset
+* patient: Added additional data to show proportions of base changes
+* create.scatterplot: Added example using error bars
+* scientific.notation: Now returns either an expression or list
+* Updated test-suite to save a single multiplot to file
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.14 2014-05-28
+
+MINOR UPDATE
+* Updated test suite to remove soon-to-be deleted plotting functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.13 2014-05-23
+
+MINOR UPDATE
+* Formatted examples in documentation to contain less than 100 characters per line
+* SNV: changed encoding of dataset to use numerical values instead of character values
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.12 2014-05-22
+
+MINOR UPDATE
+* create.violin.plot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.11 2014-05-22
+
+MINOR UPDATE
+* create.stripplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.10 2014-05-22
+
+MINOR UPDATE
+* create.stripplot: Exposing xat and xlimits parameter to allow for customization of horizontal plots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.9 2014-05-22
+
+MINOR UPDATE
+* create.segplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.8 2014-05-21
+
+MINOR UPDATE
+* create.scatterplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.7 2014-05-21
+
+MINOR UPDATE
+* Removed old datasets and updated documentation examples to use newly formatted data
+* Set LazyData in DESCRIPTION to 'yes' so that datasets can be referenced by name alone
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.6 2014-05-21
+
+MINOR UPDATE
+* CNA, SNV, microarray, patient: Added new datasets to data/ folder, each with a corresponding Rd file
+* Deleted old 'p value' dataset formerly used for create.manhattanplot examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.5 2014-05-21
+
+MINOR UPDATE
+* create.colourkey: Fixed formatting in documentation to fit under 90 characters per line
+* create.histogram: Updated example code to check dataset size instead of use hard-coded values
+* microarray: Decreased size of microarray dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.4 2014-05-20
+
+MINOR UPDATE
+* create.colourkey: Exposed parameter for colourkey cex
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.3 2014-05-20
+
+MINOR UPDATE
+* create.qqplot.fit: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.2 2014-05-20
+
+MINOR UPDATE
+* create.qqplot.comparison: Updated example plots to use standard dataset
+* MultiPlotTutorial: Reduced file size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.1 2014-05-19
+
+MINOR UPDATE
+* create.polygon: Updated example plots to use standard dataset
+
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.3.0 2014-05-16
+
+MINOR UPDATE
+* run_plots: Added test script to package
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.40 2014-05-16
+
+MINOR UPDATE
+* create.histogram: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.39 2014-05-16
+
+MINOR UPDATE
+* create.hexbinplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.38 2014-05-16
+
+MINOR UPDATE
+* create.dotmap: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.37 2014-05-15
+
+MINOR UPDATE
+* create.densityplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.36 2014-05-15
+
+MINOR UPDATE
+* create.boxplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.35 2014-05-15
+
+MINOR UPDATE
+* create.heatmap: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.34 2014-05-15
+
+BUG FIXES
+* create.heatmap: Fixed error where heatmap threw error if symbols were added, but not 'border' symbols
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.33 2014-05-15
+
+MINOR UPDATE
+* create.heatmap: Added clarification to documentation that 'colour.alpha' can be set to 'automatic'
+* create.multiplot: Expose parameters for x-axis and y-axis tick mark lengths
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.32 2014-05-14
+
+MINOR UPDATE
+* create.violinplot: Removed error message for using pch>=21 with lattice version 20-13
+* create.violinplot: Modified handling of border and fill colours for extra points
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.31 2014-05-13
+
+MINOR UPDATE
+* create.manhattanplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.30 2014-05-12
+
+MINOR UPDATE
+* create.barplot: Updated example plots to use standard dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.29 2014-05-12
+
+MINOR UPDATE
+* create.dotmap: enabled default behaviour for NA values to plot 'X' characters size 7
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.28 2014-05-12
+
+MINOR UPDATE
+* create.dotmap: Improved handling of multiple pch with multiple fill colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.27 2014-05-08
+
+MINOR UPDATE
+* create.dotmap: Deleted warning for using pch>=21 with lattice version 20-13 (outdated)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.26 2014-05-02
+
+MINOR UPDATE
+* create.dotmap: Stopped printing of warning regarding using pch>=21 with lattice version 20-13
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.25 2014-04-25
+
+MINOR UPDATE
+* Fixed spelling errors in documentation and code
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.24 2014-04-24
+
+MINOR UPDATE
+* embed.plot: Added example & updated documentation to use proper parameters
+* create.hexbinplot: Fixed formatting issue
+* create.scatterplot: Fixed auto-sensing of labels
+* create.barplot: Added functionality of adding text above bars
+* create.heatmap: Added ability to have multi-sized borders
+* create.heatmap: Adjusted input of 'main' to accept non-list values
+* MultiPlotTutorial: Compressed pdf
+* Updated formatting of all function documentation
+* NAMESPACE: Added imports
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.23 2014-04-17
+
+MINOR UPDATE
+* create.densityplot: Added data-sensing
+* create.scatterplot: Added data-sensing
+* create.hexbinplot: Added example of multi-colour scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.22 2014-04-17
+
+MINOR UPDATE
+* create.densityplot: Expose top, bottom, left, and right padding parameters
+* create.hexbinplot: Expose top, bottom, left, and right padding parameters
+* create.qqplot.fit: Expose top, bottom, left, and right padding parameters
+* create.qqplot.comparison: Expose top, bottom, left, and right padding parameters
+* create.violin.plot: Expose top, bottom, left, and right padding parameters
+* create.heatmap: Added removal of top bar in stratified dendrograms
+
+BUG FIXES
+* Fixed bugs, typos, and  mismatches in multiplot tutorial sample code
+* create.heatmap: Fixed coding issues
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.21 2014-04-13
+
+MINOR UPDATE
+* embed.plot: Added new function to allow for plot-within-a-plot layouts
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.20 2014-04-13
+
+MINOR UPDATE
+* create.heatmap: Added ability to automatically estimate values for colour.alpha parameter
+* create.heatmap: Added example for automatic colour.alpha value estimation
+
+BUG FIXES
+* create.heatmap: Fixed grid to also draw lines on first row & column
+* create.barplot: Fixed default units to inches
+* create.heatmap: Fixed documentation to match changes in code
+* create.boxplot: Fixed naming issue
+* create.multiplot: Fixed naming conventions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.19 2014-04-04
+
+MINOR UPDATE
+* Added new function 'colour.gradient' to generate sequential colour palettes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.18 2014-03-31
+
+MINOR UPDATE
+* create.heatmap: Added ability to stratify dendrogram
+* create.boxplot: Added ability to reorder boxplots based on median values
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.17 2014-03-26
+
+MINOR UPDATE
+* create.barplot: Added ability to draw curves
+* create.boxplot: Added ability to draw curves
+* create.barplot.with.error: Adjusted whisker length to not cover whole bar
+* create.heatmap: Added example of per-cell font characteristics
+* create.barplot: Added example of grouped labels
+* create.boxplot: Added option of drawing line either in front of or behind plot
+
+BUG FIXES
+* create.heatmap: Fixed issue with symbols
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.16 2014-03-17
+
+MINOR UPDATE
+* create.heatmap: Added global covariate outline
+* create.barplot: Added grouping of labels for grouped barplot
+* create.heatmap: Added examples
+* create.multiplot: Added examples
+
+BUG FIXES
+* write.metadata: Fixed to stop printing warnings
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.15 2014-03-14
+
+MINOR UPDATE
+* create.multiplot: Added ability to retrieve plot labels & limits from 'original' plots
+* create.multiplot: Updated examples
+
+BUG FIXES
+* scientific.notation.expr: Fixed issue & code formatting
+* write.metadata: Fixed issue with dependencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.14 2014-03-05
+
+MINOR UPDATE
+* create.heatmap: Added functionality of inserting additional symbols
+* create.heatmap: Added example to documentation of symbol usage
+* create.scatterplot: Changed ablines to be drawn in front of plot
+* Added datasets files to inst folder for later use in examples
+* Added vignettes folder containing multiplot tutorial
+
+BUG FIXES
+* create.barplot: Fixing reordering of bars
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.13 2014-02-26
+
+MINOR UPDATE
+* create.barplot: Set default reordering to FALSE
+* create.dotmap: Added functionality to change dot colour
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.12 2014-02-25
+
+MINOR UPDATE
+* create.barplot: Added functionality to reorder bars to be increasing or decreasing
+* create.hexbinplot: Added more examples
+* Exposed 'fontface' parameter in all plotting functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.11 2014-02-23
+
+MINOR UPDATE
+* display.statistical.result: Updated defaults in documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.10 2014-02-06
+
+MINOR UPDATE
+* create.hexbinplot: Added background colour
+* create.hexbinplot: Added ability to have tick marks on top x axis only
+* create.hexbinplot: Enabled svg output
+* create.hexbinplot: Added examples to documentation
+
+BUG FIXES
+* create.barplot: Removed origin from panel call to enable creation of stacked, horizontal, unidirectional plots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.9 2014-02-03
+
+MINOR UPDATE
+* display.statistical.result: Added option to change ":" to a different symbol
+* create.hexbinplot: Added ability to change background colour
+* create.heatmap: Added ability to display tick marks on top axis only
+* Enabled svg output for all plots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.8 2014-01-27
+
+MINOR UPDATE
+* Re-added package
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.7 2014-01-10
+
+MAJOR UPDATE
+* Added create.manhattanplot function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.4 2013-11-22
+
+MINOR UPDATE
+* Added TODO file
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.3 2013-11-18
+
+MINOR UPDATE
+* create.boxplot: Added ability to draw rectangle panels
+* create.boxplot: Added new example with grey shading between different boxes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.2 2013-11-13
+
+MINOR UPDATE
+* create.barplot: Added ability to change the width of the box
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.1 2013-11-13
+
+MINOR UPDATES
+* create.barplot: Added new parameters - background.col and draw.grid
+* create.barplot: Added new example of grey background with white grid lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.2.0 2013-11-12
+
+MINOR UPDATE
+* default.colours: Changed default qualitative palette to have brighter colours, and 12 options instead of only 9. Previous qualitative palette still accessible by setting palette.type = 'old.qual'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.8 2013-11-11
+
+MINOR UPDATES
+* default.colours: Removed deprecated survival colour scheme
+* Changed warning about greyscale compatibility to be more general
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.7 2013-11-11
+
+MINOR UPDATES
+* default.colours: Removed deprecated old chromosome colour scheme
+* Replaced 'sandybrown' with 'tan1' in new chromosome palette
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.6 2013-11-11
+
+MINOR UPDATE
+* Added create.colourkey to NAMESPACE
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.5 2013-11-10
+
+MINOR UPDATE
+* Update and reorder NAMESPACE
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.4 2013-11-09
+
+MINOR UPDATE
+* Removed unnecessary requires in get.corr.key
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.3 2013-11-09
+
+MINOR UPDATE
+* Updated minimum required versions of dependencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.2 2013-11-09
+
+MINOR UPDATES
+* create.barplot: Updated manual to reflect addition of 'axis.fontface' argument
+* create.colourkey: Removed 'enable.warnings' argument
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.1 2013-11-08
+
+MINOR UPDATE
+* create.barplot: Added arguments 'xaxis.fontface' and 'yaxis.fontface'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.1.0 2013-11-05
+
+MAJOR UPDATE
+* Added new function: 'create.colourkey' to generate and draw colourkey
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.7 2013-11-04
+
+MINOR UPDATES
+* create.stripplot: New arguments 'xaxis.fontface', 'yaxis.fontface' to allow for modification of axis tck label font face
+* create.stripplot: New argument 'ylab.axis.padding' allows for modification of padding between  yaxis label and tck labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.6 2013-11-01
+
+MINOR UPDATES
+* create.dendrogram: Updated documentation for jaccard usage
+* create.heatmap: Updated documentation for jaccard usage
+* create.heatmap: Moved logic for x.tck out of level plot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.5 2013-10-25
+
+MINOR UPDATES
+* create.heatmap: Refactoring and cleanup of code
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.4 2013-10-21
+
+MINOR UPDATES
+* create.polygon: Added 'median.lty' (for seq power plot)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.3 2013-10-18
+
+MINOR UPDATES
+* create.hexbinplot: Changed default of 'mincnt' to 1 (from 0)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.2 2013-09-26
+
+MINOR UPDATES
+* create.scatterplot.with.error: New arguments to specify plot layout and placement - 'layout', 'as.table', 'x.spacing', 'y.spacing'
+* create.polygon: Added parameters 'axis.log' and 'yaxis.log'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.1 2013-08-26
+
+MINOR UPDATES
+* create.dotmap: Added example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 4.0.0 2013-08-13
+
+MAJOR UPDATES
+* Added 'write.metadata' function
+* Added 'description' parameter to all plotting function documentations
+* write.metadata: Added 'operating system', 'machine', 'system2'
+* create.multiplot: Updated documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.10.2 2013-07-29
+
+MINOR UPDATES
+* default.colours: Update chromosome colour scheme to be coded by letter-names rather than numbers, and using more easily-distinguished colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.10.1 2013-07-25
+
+MINOR UPDATES
+* legend.grob: Added ability to specify size (width) of legend boxes for each legend individually
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.10.0 2013-07-25
+
+MAJOR UPDATES
+* create.scatterplot: Added parameter 'axis.key.padding' to adjust spacing between y-axis and key
+* create.scatterplot: Added parameters 'add.points', 'points.x', 'points.y', 'points.col', 'points.pch', 'points.cex' - allow users to add additional points to plot area
+* create.scatterplot: Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' - allow users to add text labels to plot area
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.6 2013-07-25
+
+MINOR UPDATES
+* create.dotmap: Added padding parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.5 2013-07-19
+
+MINOR UPDATES
+* create.barplot: Adjustments to spacing and commenting
+* create.dotmap: Added ability to specify padding on all sides of plot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.4 2013-07-17
+
+MINOR UPDATES
+* create.multiplot: New argument 'axes.lwd' to specify border line thickness
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.3 2013-07-15
+
+MINOR UPDATES
+* create.multiplot: Fixed 'xlab.to.xaxis.padding' variable to change the correct parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.2 2013-07-12
+
+MINOR UPDATES
+* create.heatmap: Added ability to specify two x-axes, and gave meaning to 'x-alternating = 3' (prints tick marks on top and bottom x axes)
+* create.multiplot: Added 'xlab.to.xaxis.padding' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.1 2013-07-09
+
+MINOR UPDATES
+* create.dotmap: Replaced 'grid.colour' with 'row.colour' and 'col.colour'
+* create.barplot: Updated to accept arguments that handle background shading
+* create.heatmap: Added 'xaxis.tck' and 'yaxis.tck' parameters to override default values based on covariate size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.9.0 2013-07-04
+
+MINOR UPDATES
+* create.multiplot: Added 'layout.skip' parameter to allow for blank spots in layout, and also added a complex example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.7 2013-06-28
+
+MINOR UPDATES
+* rgb.to.greyscale: Changing function to return results, rather than print
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.6 2013-06-27
+
+MINOR UPDATES
+* append.footnote: Added function to create plot footnotes
+* default.colours: Fixed method of returning one-colour palettes for backwards compatibility
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.5 2013-06-17
+
+MINOR UPDATES
+* default.colours: Adjustments to chromosome colour palette
+* default.colours: Added ability to provide multiple sequential and binary colour schemes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.4 2013-06-13
+
+MINOR UPDATES
+* create.boxplot: Added ability to define 'abline.v'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.3 2013-06-12
+
+MINOR UPDATES
+* display.colours: Added function to view colour palettes and what they look like in grey scale
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.2 2013-06-11
+
+MINOR UPDATES
+* covariates.grob: Added 'reorder.grid.index' parameter to specify ordering of grid indices
+* create.heatmap: Added 'covariates.reorder.grid.index' and 'covariates.top.reorder.grid.index' parameters to match changes to covariates.grob
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.1 2013-06-10
+
+MINOR UPDATES
+* create.heatmap: Split 'grid.colour' and 'grid.lwd' parameters into 'row.colour/col.colour' and 'row.lwd/col.lwd'
+* create.heatmap: Added grandfather parameters for 'grid.colour' and 'grid.lwd'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.8.0 2013-06-04
+
+MAJOR UPDATES
+* colour.to.grey: Added new function to convert R colours to R grey colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.7.0 2013-05-29
+
+MAJOR UPDATES
+* create.heatmap: Added 'covariates.row.lines', 'covariates.col.lines', 'covariates.top.row.lines', 'covariates.top.col.lines' corresponding to new covariates.grob arguments, and updated examples
+* covariates.grob: Added parameters 'row.lines' and 'col.lines' to allow user to specify which grid lines to draw in covariate bars, and updated examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.20 2013-04-23
+
+MINOR UPDATES
+* get.corr.key: New arguments to allow for the addition of a title to the key
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.19 2013-04-04
+
+MINOR UPDATES
+* create.barplot: Attempting to make sizes match up
+* create.dotmap: Can now have custom colours specified
+* write.plot: Code formatting changes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.18 2013-03-19
+
+MINOR UPDATES
+* create.barplot: Code clean-up to match coding standards
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.17 2013-03-12
+
+MINOR UPDATES
+* create.barplot: Fix to align error bars when barplot is grouped
+* write.plot: Refactor to place extension-specific code in inst/ext2function.txt
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.16 2013-03-07
+
+MINOR UPDATES
+* write.plot: Allowing pdf and png output
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.15 2013-03-05
+
+MINOR UPDATES
+* create.segplot: Added 'abline.h' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.14 2013-03-01
+
+MINOR UPDATES
+* create.heatmap: Centralize parameter-checking code at start of script
+* Added pch>=21 warning to appropriate R files, and removed ^M
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.13 2013-02-19
+
+MINOR UPDATES
+* create.polygon: Added line plotting options 'add.xyline', 'abline.h', 'abline.v'
+* create.barplot: Added examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.12 2013-02-14
+
+MINOR UPDATES
+* create.multiplot: Added check for NAs in the legends workaround
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.11 2013-02-12
+
+MINOR UPDATES
+* create.multiplot: Added workaround for lattice being unable to accept multiple legends with the same name via update.trellis
+* create.multiplot: Allowed x/y-relations between plots to be set
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.10 2013-02-06
+
+MINOR UPDATES
+* create.multiplot: Added 'xlab.padding', and 'key.bottom.padding'
+* Added copyright header to R files
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.9 2013-01-30
+
+MINOR UPDATES
+* create.barplot: Updating with "raster" command
+* create.multiplot: Making examples prettier, moving key.bottom.padding into argument
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.8 2013-01-30
+
+MINOR UPDATES
+* create.barplot: Merging with create.barplot.with.error
+* create.barplot.with.error: Merging with create.barplot
+* create multiplot: Adding 'xaxis.fontface', 'yaxis.fontface' to allow for specification of axis-label fontface
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.7 2013-01-23
+
+MINOR UPDATES
+* create.scatterplot: Added explicit horizontal argument
+* create.barplot: Added options to specify distance between x-axis and label
+* create.scatterplot: Add options to pass arbitrary plots onto lattice:xyplot
+* create.barplot.with.error: Fixing documentation
+* create.barplot: Allow user to edit 'key.bottom'
+* create.stripplot: Added parameters to allow for different border/fill colours (for pch 21:25), 'colour.alpha' to allow for plotting character transparencies, 'as.table', 'x.spacing', 'y.spacing' for customization of panels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.6 2013-01-09
+
+MINOR UPDATES
+* create.dotmap: Added argument 'pch.border.col' to set colour of dot border if pch is 21:25
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.5 2013-01-09
+
+MINOR UPDATES
+* create.scatterplot: Added 'key.left.padding' parameter to place legends to left of graph
+* create.scatterplot: Added 'axes.lty' to set line style of axes lines
+* force.colour.scheme: Added another colour palette
+* create.multiplot: Added three parameters - 'xaxis.rot', 'key.left.padding', 'key.right.padding'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.4 2012-12-14
+
+MINOR UPDATES
+* create.heatmap: Added option of including x and y axis label covariates (between label and heatmap), and examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.3 2012-12-14
+
+MINOR UPDATES
+* force.colour.scheme: Added alternative colour scheme for annovar output
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.2 2012-12-12
+
+MINOR UPDATES
+* get.corr.key: Added missing else case for beta1.p
+* force.colour.scheme: Added synonymous SNV to the list
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.1 2012-12-11
+
+MINOR UPDATES
+* create.multiplot: Changed key.left value to 1 so that legends can be placed to left of multiplot area
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.6.0 2012-12-11
+
+MAJOR UPDATES
+* create.scatterplot: Added ability to draw rectangles in background
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.17 2012-12-09
+
+MINOR UPDATES
+* create.polygon: Changed default values of 'xgrid.at' and 'ygrid.at'
+* create.polygon: Added 'xaxis.fontface' and 'yaxis.fontface'
+* create.polygon: Added 'fontface = xaxis.fontface' and 'fontface = yaxis.fontface' to scales$x and scales$y
+* create.polygon: Added example to demonstrate use with legend.grob
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.16 2012-12-08
+
+MINOR UPDATES
+* create.polygon: Adjusted values of par.settings$layout.widths$axis.key.padding and par.settings$layout.heights$axis.key.padding to equal 1 - this lets the legend on the right be properly rendered
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.15 2012-12-07
+
+MINOR UPDATES
+* create.barplot: Added ability to create horizontal barplots - 'plot.horizontal', 'xlimits', and 'xat' parameters added & example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.14 2012-12-07
+
+MINOR UPDATES
+* create.scatterplot: Fixing example to adjust placement of yaxis title
+* create.dotmap: Adding parameter 'fill.colour' to allow user to fill background of cells
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.13 2012-11-28
+
+MINOR UPDATES
+* force.colour.scheme: Added overload functionality, changed scheme
+* Updating date with version
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.12 2012-11-28
+
+MINOR UPDATES
+* force.colour.scheme: Added new force colour scheme function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.12 2012-11-26
+
+MINOR UPDATES
+* create.barplot: Added ability to draw vertical lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.11 2012-11-26
+
+MINOR UPDATES
+* create.multiplot: Updated documentation to show to remove tick marks
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.10 2012-11-26
+
+MINOR UPDATES
+* get.line.breaks: Added get line breaks function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.9 2012-11-23
+
+MINOR UPDATES
+* create.heatmap: Added check for features exceeding pixels/width
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.8 2012-11-23
+
+MINOR UPDATES
+* create.polygon: Reverted functionality back to using if statements instead of ternary operators
+* create.heatmap: Added covariate bar between heatmap and xaxis labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.7 2012-11-13
+
+MINOR UPDATES
+* create.dotmap: Added 'grid.col.lwd' and 'grid.row.lwd' to allow different weights of gridlines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.6 2012-11-13
+
+MINOR UPDATES
+* create.dotmap: Updated 'key.left', 'key.right', 'key.bottom' to default to 1 so that legends/keys are properly incorporated
+* create.dotmap: Added example using covariate bar and legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.5 2012-11-08
+
+MINOR UPDATES
+* create.heatmap: Use grobPack() fontfamily specification to avoid unknown Arial font specification
+* create.dotmap: Changed yaxis label default to not be bold
+* legend.grob: Added parameters - 'layout', 'between.col', 'between.row' to allow user to specify layout for multiple legends and set empty space between rows/columns
+* legend.grob: Changed titles in legend to use a text grob instead of draw.key
+* create.heatmap: Added 'legend.layout', 'legend.between.col', and 'legend.between.row' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.4 2012-11-02
+
+MINOR UPDATES
+* create.dotmap: Updated to use dotmap colour scheme by default, fixed palette creation for >3 colour schemes
+* create.dotmap: Added example with 5-colour background
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.3 2012-10-30
+
+MINOR UPDATES
+* create.heatmap: Added set.seed() call at beginning of examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.2 2012-10-29
+
+MINOR UPDATES
+* create.scatterplot: Fixed codoc error
+* General fixes for coding-style standardization and document fixes
+* Updates to dependency versions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.1 2012-10-26
+
+MINOR UPDATES
+* create.scatterplot: Changed default curves to use min/max with na.rm=T
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.5.0 2012-10-10
+
+MAJOR UPDATES
+* covariates.grob: Added parameters 'grid.row', 'grid.col', 'grid.border' to allow customization of grid lines within covariate bars
+* create.heatmap: Added parameters 'covariates.grid.row', 'covariates.grid.col', 'covariates.grid.border', 'covariates.top.grid.row', 'covariates.top.grid.col', 'covariates.top.grid.border', 'legend.border', 'legend.border.padding'
+* create.heatmap: Added parameters 'covariates.padding', and 'covariates.top.padding' to allow for empty space between covariate bars and dendrograms
+* legend.grob: Added parameters 'border', 'border.padding' to allow for border around legend
+* Updated examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.4.4 2012-10-10
+
+MINOR UPDATES
+* display.statistical.result: Added space before and after "x" sign
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.4.3 2012-10-10
+
+MINOR UPDATES
+* create.heatmap: Changed 'grid.row' and 'grid.col' to default to false
+* create.heatmap: No longer assumes that matrices with less than 125 rows/columns should have grid lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.4.2 2012-10-02
+
+MINOR UPDATES
+* display.statistical.result: Migrating this function to plotting.general
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.4.1 2012-09-25
+
+MINOR UPDATES
+* create.heatmap: Added code to close devices opened by the grid::covertUnit function and remove Rplots.pdf files if necessary
+* legend.grob: Added code to remove Rplots.pdf files created by the lattice::draw.key
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.4.0 2012-09-12
+
+MAJOR UPDATES
+* default.colours: Added gender colour palette
+* create.dendrogram: Interface change - renamed cluster.dimensions (pl.) to cluster.dimension (s.) because only takes scalars
+* create.dendrogram: Code clean-up
+* create.dendrogram: Fixed handling of jaccard distance
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.7 2012-09-10
+
+MINOR UPDATES
+* create.segplot: Removed warning caused by typo in man file
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.6 2012-08-30
+
+MINOR UPDATES
+* legend.grob: Added code to close extra device created by the draw.key()
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.5 2012-08-29
+
+MINOR UPDATES
+* create.densityplot: Set groups to an ordered factor (avoids auto-alphabetical ordering by lattice during plotting)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.4 2012-08-24
+
+MINOR UPDATES
+* create.polygon: Added example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.3 2012-08-20
+
+MINOR UPDATES
+* create.segplot: Removed unused parameter from function definition & fixed inconsistencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.2 2012-08-20
+
+MINOR UPDATES
+* create.boxplot: Replaced call to panel.BL.bwplot with call to panel.bwplot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.1 2012-08-17
+
+MINOR UPDATES
+* default.colours: Added new 2-colour scheme for dotmaps
+* create.dotmap: Updated example to use new dotmap colour scheme from default.colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.3.0 2012-08-17
+
+MINOR UPDATES
+* create.segplot: Added new function to create segplots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.31 2012-08-16
+
+MINOR UPDATES
+* create.heatmap: Added notes in help file for using euclidean when lots of ties and correlation fails
+* legend.grob: Added notes in help file for using euclidean when lots of ties and correlation fails
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.30 2012-08-14
+
+MINOR UPDATES
+* create.violinplot: Fixed a bug in extra points argument
+* create.scatterplot: Added alpha argument to control plotting transparency
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.29 2012-08-14
+
+MINOR UPDATES
+* create.dendrogram: Updated to use dist(method = "jaccard") instead of jaccard.distance()
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.28 2012-08-07
+
+MINOR UPDATES
+* default.colours: Changed warning message when survival colour scheme is used with more than 5 colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.27 2012-08-02
+
+MINOR UPDATES
+* create.polygon: Fixed border.col argument to allow different coloured borders for multiple groups
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.26 2012-07-31
+
+MINOR UPDATES
+* create.dendrogram: Changed jaccard.distance to use 't(x)' instead of 'x' in order to imitate behaviour of dist function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.25 2012-07-26
+
+MINOR UPDATES
+* create.polygon: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
+* create.polygon: New arguments 'xgrid.at', 'ygrid.at', 'grid.col' to allow for grid lines in the background of the main plot
+* create.violin.plot: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
+* create.violin.plot: New arguments 'fill.colour', 'border.lwd' to allow for control of interior colours and exterior border widths
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.24 2012-07-25
+
+MINOR UPDATES
+* create.scatterplot.with.error: New arguments 'strip.col', 'strip.cex' to control size and background colour of panel labels
+* create.scatterplot.with.error: New argument 'error.bar.length' to adjust size of error bar whiskers
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.23 2012-07-25
+
+MINOR UPDATES
+* create.stripplot: Added parameters for groups, layout, padding around graph, key and legend, and example for how to use 'groups' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.22 2012-07-23
+
+MINOR UPDATES
+* default.colours: Changed greyscale warning message for survival palette
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.21 2012-07-23
+
+MINOR UPDATES
+* create.barplot: Added example using covariates with labels/covariate legend
+* create.scatterplot: Added example using covariates with labels/covariate legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.20 2012-07-22
+
+MINOR UPDATES
+* create.heatmap: Resolved codoc mismatch introduced in v3.2.19
+* Updated package dependencies to newer versions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.19 2012-07-20
+
+MINOR UPDATES
+* create.heatmap: Replaced arguments 'border' and 'border.lwd' with 'grid.colour' and 'grid.lwd'
+* create.heatmap: Added ability to turn off interior gridlines using 'grid.row=FALSE', 'grid.col=FALSE' or 'grid.lwd=0'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.18 2012-07-17
+
+MINOR UPDATES
+* create.dendrogram: Updated to use jaccard.distance instead of vegdist
+* Removed vegan dependency from DESCRIPTION
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.17 2012-07-17
+
+MINOR UPDATES
+* panel.BL.bwplot: Changed 'nr' to 'nrow' in matrix call to avoid check warnings
+* default.colours: Changed colours in survival palette
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.16 2012-07-17
+
+MINOR UPDATES
+* get.corr.key: Added robust regression coefficients and example using outlier
+* Added dependency on package MASS
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.15 2012-07-16
+
+MINOR UPDATES
+* Changing vegan dependency version to be lower
+* default.colours: Added survival palette and explanation in file as to how to add a new palette
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.14 2012-07-12
+
+MINOR UPDATES
+* default.colours: Code clean-up and added ability to use chromosome colour scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.13 2012-07-03
+
+MINOR UPDATES
+* get.corr.key: Changed default resolution in create.survival.plot from 2000 to 100
+* create.histogram: Added support for horizontal and vertical abline
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.12 2012-06-28
+
+MINOR UPDATES
+* default.colours: Fixed return value for Venn diagram palettes to return a list of both fill colours and text colours, as per example in documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.11 2012-06-27
+
+MINOR UPDATES
+* create.heatmap: Added 'text.col' parameter
+* create.heatmap: Added example of using unicode symbols instead of text - similar to dotmap, but allows clustering
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.10 2012-06-26
+
+MINOR UPDATES
+* create.heatmap: Correct ordering of text in clustered data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.9 2012-06-15
+
+MINOR UPDATES
+* create.scatterplot: Reordered 'legend' and 'layout.width' arguments to fix padding issues
+* create.scatterplot.with.error: Reordered 'legend' and 'layout.width' arguments to fix padding issues
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.8 2012-06-12
+
+MINOR UPDATES
+* create.stripplot: Added 'jitter' argument to allow for staggering of data along x-axis
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.7 2012-06-08
+
+MINOR UPDATES
+* create.histogram: Added parameters for padding, spacing, layout, panel
+* create.histogram: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
+* covariates.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
+* create.multiplot: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
+* legend.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.6 2012-06-05
+
+MINOR UPDATES
+* create.scatterplot: Added option 'abline.v' to draw vertical lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.5 2012-05-31
+
+MINOR UPDATES
+* create.densityplot: Fixed bug when grids are added - now if type=c("g","l"), xyplot.panels do not double call "g" circle symbols instead of lines
+* create.multiple.boxplots: Updated x-axis label/rotation variable names to match other plotting functions & added argument to allow for specification of main.cex
+* create.stripplot: Updated x-axis rotation variable name to match other plotting functions & added arguments to specify x/ylab.col, x/yaxis.col/tck/rot
+* create.violinplot: Updated x-axis label/rotation variable names to match other plotting functions & added arguments to allow for specification of x/ylab.col, x/yaxis.col/tck/rot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.4 2012-05-29
+
+MINOR UPDATES
+* create.histogram: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
+* create.polygon: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
+* create.qqplot.comparison: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
+* create.qqplot.fit: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
+* create.scatterplot: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
+* create.scatterplot.with.error: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.3 2012-05-28
+
+MINOR UPDATES
+* create.barplot: Added example with covariates
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.2 2012-05-28
+
+MINOR UPDATES
+* create.multiplot: Adjusted formatting and removed debugging code
+* create.scatterplot: Added option 'abline.v' to draw vertical lines
+* create.heatmap: Updated x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'main.cex
+* create.hexbinplot: Updated x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'xaxis.tck', 'yaxis.tck'
+* create.dotmap: Updated x/y label and x/y cex variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.1 2012-05-18
+
+MINOR UPDATES
+* create.multiplot: Clarified labels on 6 panel example
+* create.barplot: Updated examples to use new variables
+* create.densityplot: Updated examples to include new variables
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.2.0 2012-05-16
+
+MAJOR UPDATES
+* create.multiplot: Added example with 6 panels & modified variable names to be consistent
+* create.barplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
+* create.barplot.with.error: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
+* create.boxplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
+* create.densityplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.16 2012-05-15
+
+MINOR UPDATES
+* create.stripplot: Implemented customizable character colour
+* create.multiple.stripplots: Implemented customizable character colour
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.15 2012-05-14
+
+MINOR UPDATES
+* create.multiplot: Improved consistency of test output file names and variable names
+* create.densityplot: Changed defaults to not display axis lines
+* create.hexbinplot: Changed defaults to not display axis lines
+* create.scatterplot.with.error: Changed defaults to not display axis lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.14 2012-05-11
+
+MINOR UPDATES
+* create.dotmap: Added 'xaxis.lab.cex' and 'yaxis.lab.cex' parameters to specify size of axis labels
+* create.dotmap: Added 'key.top' parameter to specify size of space between colourkey and xaxis.label
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.13 2012-05-01
+
+MINOR UPDATES
+* create.heatmap: Added 'axes.lwd' parameter to change border width
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.12 2012-04-25
+
+MINOR UPDATES
+* create.multiplot: Added example combining a stripplot and heatmap
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.11 2012-04-23
+
+MINOR UPDATES
+* create.heatmap: Added 'xat' and 'yat' parameters to specify label locations
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.10 2012-04-20
+
+MINOR UPDATES
+* create.scatterplot: Added horizontal abline parameter - able to specify line width and type
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.9 2012-04-19
+
+MINOR UPDATES
+* create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
+* create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
+* create.heatmap: Added example using covariate legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.8 2012-04-18
+
+MINOR UPDATES
+* create.heatmap: Updated parameter for cell text font size & clarified definitions of 'row.lines' and 'col.lines'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.7 2012-04-13
+
+MINOR UPDATES
+* create.heatmap: Added parameters to control text in cells and to manually specify row/column grid vectors
+* legend.grob: Added parameter to specify border colour of legends
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.6 2012-04-12
+
+MINOR UPDATES
+* create.multiplot: Improved legend functionality
+* create.heatmap: Added ability to insert text in cells & added example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.5 2012-04-08
+
+MINOR UPDATES
+* create.heatmap: Added parameters 'title.just' and 'title.fontface' to customize legend titles
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.5 2012-04-03
+
+MINOR UPDATES
+* create.heatmap: Edited documentation to finalize examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.4 2012-04-02
+
+MINOR UPDATES
+* create.multiplot: Added parameters for more customization - 'main.cex', 'xlab.cex', 'ylab.cex', 'xlimits', 'ylimits'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.3 2012-04-19
+
+MINOR UPDATES
+* create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
+* create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
+* create.heatmap: Added example using covariate legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.2 2012-03-30
+
+MINOR UPDATES
+* create.heatmap: Updated examples to be fewer and follow a logical progression
+* covariates.grob: Updated examples to be generated using grid.draw() and produce .tiff output
+* legend.grob: Prevented premature closure of user images by removing "dev.off()" call & updated examples to .tiff files using grid.draw()
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.1 2012-03-21
+
+MINOR UPDATES
+* create.hexbinplot: Altered layout.widths to automatically adjust key.right if colourkey is added (previously right.padding was adjusted and legend was occasionally cut off)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.1.0 2012-03-16
+
+MAJOR UPDATES
+* create.heatmap: Added ability to take more than three colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.9 2012-03-15
+
+MINOR UPDATES
+* create.heatmap: Added parameters 'shrink', 'border', 'border.lwd'
+* create.multiplot: Updated example to use create.heatmap instead of base lattice::levelplot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.8 2012-03-09
+
+MINOR UPDATES
+* create.heatmap: Added parameter 'force.clustering' to allow user to ignore the row-limitation
+* create.dendrogram: Added parameter 'force.clustering' to allow user to ignore the row-limitation
+* Updated dependency versions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.7 2012-03-09
+
+MINOR UPDATES
+* create.histogram: Removed check of 'x' to ensure it is a formula - problematic is function is called within another function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.6 2012-02-21
+
+MINOR UPDATES
+* create.multiplot: Changing default of 'xaxis.alternating' parameter
+* Modified "see also" documentation of plotting functions  to include web versions of lattice graphics
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.5 2012-02-15
+
+MINOR UPDATES
+* Added "see also" sections of documentation of plotting functions for easy referencing
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.4 2012-02-10
+
+MINOR UPDATES
+* create.multiplot: Added 'panel.widths' parameter & an example to the documentation
+* create.multiplot: Removed internal axes labels in cases where plot axes are identical
+* create.scatterplot: Fixed file formatting to use tabs
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.3 2012-02-07
+
+MINOR UPDATES
+* create.multiplot: Fixed file formatting to use tabs instead of spaces
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.2 2012-02-02
+
+MINOR UPDATES
+* create.multiplot: Changed name of example output
+* create.heatmap: Changed default colour scheme to use two colours if data is one-sided and three colours if data is two-sided
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.1 2012-01-25
+
+MINOR UPDATES
+* create.heatmap: updated documentation to link to related man pages
+* legend.grob: updated documentation to explain implementation decisions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 3.0.0 2012-01-23
+
+MAJOR UPDATES
+* create.heatmap: Added parameters 'covariate.legends', 'legend.cex', 'legend.title.cex', and 'legend.side' to allow users to include a legend for the covariates
+* legend.grob: Added this function to draw legends
+
+MINOR UPDATES
+* Updated NAMESPACE to rename create.plot.with.levelplot to create.multiplot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.13.1 2012-01-16
+
+MINOR UPDATES
+* create.histogram: Added 'x' parameter to take in formulas, leaving 'data' parameter to take in data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.13.0 2012-01-16
+
+MAJOR UPDATES
+* create.multiplot: Renamed this function - previously called 'create.plot.with.levelplot'
+* create.multiplot: Updated to take any number of plots and display them in the specified layout
+* create.multiplot: Replaced parameters 'plot.object' and 'levelplot.object' with 'plot.objects
+* create.multiplot: Replaced parameter 'spacing' with 'yspacing'
+* create.multiplot: Added parameters 'xspacing' and 'plot.layout'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.5 2012-01-11
+
+MINOR UPDATES
+* create.barplot: Added parameter 'border.col' to control border colour
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.4 2012-01-11
+
+MINOR UPDATES
+* create.barplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.3 2012-01-11
+
+MINOR UPDATES
+* create.boxplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.2 2012-01-10
+
+MINOR UPDATES
+* create.barplot: Added 'panel.abline'
+* create.boxplot: Added 'panel.abline'
+* create.heatmap: Added parameters 'xlab', 'ylab' and ability to place x-axis label on top axis
+* create.plot.with.levelplot: Added error checking for trellis objects
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.1 2012-01-10
+
+MINOR UPDATES
+* create.heatmap: Added ability to plot covariates without dendrograms
+* create.heatmap: Added parameters 'row.dendrogram' and 'col.dendrogram' to allow users to pass in dendrograms
+* Added two functions - create.dendrogram() and covariates.grob()
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.12.0 2012-01-10
+
+MINOR UPDATES
+* get.defaults: Set unix to fall back on default fonts
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.10 2012-01-06
+
+MINOR UPDATES
+* create.plot.with.levelplot: Updated border example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.9 2012-01-04
+
+* Committing new version
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.8 2012-01-04
+
+MINOR UPDATES
+* create.plot.with.levelplot: Improved ability to control axis labels
+* create.plot.with.levelplot: Added padding parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.7 2011-12-23
+
+MINOR UPDATES
+* Minor change to DESCRIPTION
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.6 2011-12-22
+
+MINOR UPDATES
+* create.scatterplot: Updated to allow for parameters of length one specify properties of all curves with 'add.curves' option
+* create.scatterplot: Added warning for cases when curves are drawn with data containing groups where grouping variables are being removed
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.5 2011-12-16
+
+MINOR UPDATES
+* create.plot.with.levelplot: Reformatted example code
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.4 2011-12-15
+
+MINOR UPDATES
+* create.plot.with.levelplot: Improved readability of parameter list
+* create.scatterplot: Updated panel.curve code to avoid 'no visible binding for global variable x' error
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.3 2011-12-13
+
+MINOR UPDATES
+* create.scatterplot.with.error: Minor formatting fix to example
+* create.scatterplot: Added parameter 'key.top' to control spacing above the key
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.2 2011-12-13
+
+MINOR UPDATES
+* create.heatmap: Renamed parameter 'data.to.cluster' with 'x'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.1 2011-12-13
+
+MINOR UPDATES
+* create.heatmap: Cleaned up code by removing spurious print statements
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.11.0 2011-12-13
+
+MAJOR UPDATES
+* Updated many plotting examples have better clarity and use default.colours()
+
+MINOR UPDATES
+* default.colours: Standardized error-handling
+* create.dotmap: Changed default colour scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.12 2011-12-13
+
+MINOR UPDATES
+* create.heatmap: Renamed parameters 'names.row' and 'names.col' with 'xaxis.lab' and 'yaxis.lab'
+* create.heatmap: Added new parameter 'xaxis.col' to set colours of axis labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.11 2011-12-13
+
+MINOR UPDATES
+* create.heatmap: Cleaned up code by standardizing variable names and adjusting error-handling
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.10 2011-12-12
+
+MINOR UPDATES
+* optimal.heatmap.cex.txt: Improved formatting of header
+* create.heatmap: Cleaned up code
+* create.heatmap: Added example of how to specify row and column labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.9 2011-12-12
+
+MINOR UPDATES
+* create.scatterplot: Changed formatting to produce a smaller gap between title and plot
+* create.scatterplot: Updated example to include legend and filename
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.8 2011-12-06
+
+MINOR UPDATES
+* create.scatterplot: Cleaned up code by removing inverted line
+* Updated default value of 'strip.col' to 'white' instead of 'grey'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.7 2011-12-02
+
+MINOR UPDATES
+* create.scatterplot: Added example to draw colour depth to scatterpoints
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.6 2011-12-01
+
+BUG FIXES
+* create.scatterplot: Fixed bug in default behaviour for 'curve.from' and 'curve.to' parameters
+
+MINOR UPDATES
+* create.scatterplot: Updated example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.5 2011-12-01
+
+MINOR UPDATES
+* create.scatterplot: Cleaned up code
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.4 2011-11-30
+
+MINOR UPDATES
+* create.scatterplot: Replace parameter 'add.lines' with 'add.curves', this allowing the user to draw any segment of any curve that can be specified with a function
+* create.scatterplot: Added example to demonstrate use of 'add.curves' parameter
+* create.polygon: Fixed 'alternating' parameter to force x-axis labels to be on the bottom row
+* create.polygon: Updated example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.3 2011-11-29
+
+MINOR UPDATES
+* create.polygon: Updated 'top.padding' and 'bottom.padding' parameters
+* create.scatterplot: Added ability to draw line segments on plotting region
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.2 2011-11-17
+
+MINOR UPDATES
+* create.violin.plot: Updated to allow boundaries and scaling
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.1 2011-11-17
+
+MINOR UPDATES
+* create.plot.with.levelplot: Added this function by merging 'create.boxplot.with.levelplot' and 'create.scatterplot.with.levelplot'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.10.0 2011-10-27
+
+MAJOR UPDATES
+* create.scatterplot.with.levelplot: Added this function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.44 2011-10-24
+
+MINOR UPDATES
+* Temporary change to lattice dependency version
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.43 2011-10-12
+
+MINOR UPDATES
+* create.heatmap: Added parameters to support ?dist based distance measures for clustering
+* create.hexbinplot: Added warning if specified 'maxcnt' is less than the actual max count
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.42 2011-09-28
+
+MINOR UPDATES
+* create.boxplot: Updated to force axis labels to always be on the left or bottom
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.41 2011-09-27
+
+MINOR UPDATES
+* Added 'as.table' parameter to plotting functions to allow for panel ordering
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.40 2011-09-21
+
+MINOR UPDATES
+* create.qqplot.comparison: Added option of choosing difference methods to draw a reference line
+* create.qqplot.fit: Added option of choosing difference methods to draw a reference line
+* create.qqplot.fit: Added ability to draw confidence bands for grouped data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.39 2011-09-20
+
+MINOR UPDATES
+* create.dotmap: Standardized parameter names
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.38 2011-09-14
+
+MINOR UPDATES
+* create.dotmap: Added example of using 'padding.text'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.37 2011-09-13
+
+MINOR UPDATES
+* create.qqplot.fit: Added polygon plots for confidence intervals
+* create.scatterplot: Fixed 'add.axes' parameter default value in documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.36 2011-09-13
+
+MINOR UPDATES
+* create.scatterplot: Changed default value of 'add.axes' parameter to FALSE
+* default.colours: Change output format to be returned, rather than printed
+* create.polygon: Added 'use.loess.median' and 'use.loess.border' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.35 2011-09-08
+
+MINOR UPDATES
+* change dependency version for package BoutrosLab.statistics.general
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.34 2011-09-05
+
+MINOR UPDATES
+* create.barplot: Added parameters to change colour and font size of the panel title
+* create.boxplot: Added parameters to change colour and font size of the panel title
+* create.polygon: Added parameters to change colour and font size of the panel title
+* create.scatterplot: Added parameters to change colour and font size of the panel title
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.33 2011-09-01
+
+MINOR UPDATES
+* Added 'rgb.to.greyscale' function to NAMESPACE
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.32 2011-09-01
+
+BUG FIXES
+* create.hexbinplot: Removed appearance of artificial blue dot at origin
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.31 2011-09-01
+
+MINOR UPDATES
+* rgb.to.greyscale: Added function to BoutrosLab.plotting.general
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.30 2011-08-30
+
+MINOR UPDATES
+* create.qqplot.fit: Changes to ensure expected functionality
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.29 2011-08-30
+
+MINOR UPDATES
+* create.qqplot.fit: Deleted function 'single.qqplot.CI' and revised corresponding part in function 'create.qqplot.fit'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.28 2011-08-30
+
+MINOR UPDATES
+* Updated maintainer email
+* Removed dependency on package 'distr'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.27 2011-08-26
+
+MINOR UPDATES
+* create.histogram: Changed formatting of documentation
+* create.multiple.stripplots: Added 'ylab.axis.padding' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.26 2011-08-26
+
+MINOR UPDATES
+* default.colours: Added new function to provide colour schemes for plotting
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.25 2011-08-25
+
+MINOR UPDATES
+* optimal.heatmap.cex.txt: Added lookup file for setting default font sizes for heatmaps of varying size
+* create.heatmap: Changed to set default font sizes from lookup file (based on size of input)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.24 2011-08-24
+
+MINOR UPDATES
+* create.polygon: Cleaned up code
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.23 2011-08-24
+
+MINOR UPDATES
+* create.multiple.boxplots: Added 'ylab.axis.padding' and 'ylab.cex' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.22 2011-08-24
+
+MINOR UPDATES
+* create.dotmap: Changed default grid line colour to grey when no background colour is present
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.21 2011-08-23
+
+MINOR UPDATES
+* single.qqplot.CI: Removed 'subset' function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.20 2011-08-23
+
+MINOR UPDATES
+* create.qqplot.comparison: Fixed examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.19 2011-08-23
+
+MINOR UPDATES
+* create.qqplot.comparison: Fixed examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.18 2011-08-23
+
+MINOR UPDATES
+* create.qqplot.comparison: Added functionality of drawing confidence bands
+* create.qqplot.comparison: Changed label default behaviour
+* create.qqplot.fit: Changed label default behaviour
+* create.dotmap: Changed default grid line colour to black if background colour is present
+* create.polygon: Fixed grouping functionality and example
+* create.polygon: Added translucent colours
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.17 2011-08-16
+
+MINOR UPDATES
+* create.polygon: Changed input parameter settings to be more intuitive
+* create.polygon: Added examples (including grouping example)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.16 2011-08-16
+
+MINOR UPDATES
+* create.scatterplot: Removed redundancy in code by parameterizing y=x line, and changed example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.15 2011-08-15
+
+MINOR UPDATES
+* create.boxplot.with.levelplot: Added more examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.14 2011-08-13
+
+MINOR UPDATES
+* create.qqplot.fit: Improvements to code formatting
+* create.qqplot.comparison: Improvements to code formatting
+* single.qqplot.CI: Improvements to code formatting
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.13 2011-08-11
+
+MINOR UPDATES
+* create.hexbinplot: Added 'xaxis.labels' and 'yaxis.labels' parameters
+* create.boxplot.with.levelplot: Improved example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.12 2011-08-11
+
+MINOR UPDATES
+* create.barplot: Added panel parameters
+* create.scatterplot: Added panel parameters and improved input method of 'groups' parameter
+* boxplot.with.levelplot: Cleaned up example names
+* create.polygon: Cleaned up example names
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.11 2011-08-10
+
+MINOR UPDATES
+* create.scatterplot: Added 'layout' and 'xaxis.tck' parameters to specify figure arrangement and length of tick marks
+* create.scatterplot: Added example to show lines connecting dots to the x-axis
+* get.corr.key: Added 'key.cex' parameter to allow users to specify font size of the key
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.10 2011-08-08
+
+MINOR UPDATES
+* create.qqplot.fit: Added example
+* single.qqplot.CI: Renamed from 'qq.single.CI' and updated examples and documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.9 2011-08-08
+
+MINOR UPDATES
+* qq.single.CI: Renamed from 'envelop' function
+* create.qqplot.comparison: Renamed from 'create.qqplot2' function
+* create.qqplot.fit: Renamed from 'create.qqplot' function
+* create.scatterplot: Updated example output names for consistency
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.8 2011-08-06
+
+MINOR UPDATES
+* create.qqplot: Code-review
+* create.qqplot2: Code-review
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.7 2011-08-05
+
+MINOR UPDATES
+* envelope: Added function to create one-sample qqplot
+* create.qqplot: Updated code and documentation
+* create.qqplot2: Updated code and documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.6 2011-08-05
+
+MINOR UPDATES
+* create.qqplot2: Added function to create two-sample qq plots
+* create.qqplot: Added function to create one-sample qq plots
+* create.boxplot.with.levelplot: Updated documentation
+* create.polygon: Updated documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.5 2011-08-03
+
+MINOR UPDATES
+* create.heatmap: Added 'print.color.key' parameter to enable turning "off" of colourkey printing
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.4 2011-08-03
+
+MINOR UPDATES
+* create.boxplot.with.levelplot: Added new function
+* create.polygon: Added new function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.3 2011-08-02
+
+MINOR UPDATES
+* create.violin.plot: Updated examples
+* Updated package dependencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.2 2011-07-25
+
+MINOR UPDATES
+* create.dotmap: Updated documentation
+* Updated package dependencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.1 2011-07-23
+
+MINOR UPDATES
+* create.boxplot: Added 'x.tck' parameter to control length of tick marks
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.9.0 2011-07-21
+
+MINOR UPDATES
+* create.dotmap: Added new plotting function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.8.3 2011-07-14
+
+MINOR UPDATES
+* create.boxplot: Added panel parameters
+* create.heatmap: Added 'x.alternating' parameter to control position of x-axis labels
+* Added warning to documentation of plotting functions to alert users of ineffective methods of running functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.8.2 2011-06-27
+
+MINOR UPDATES
+* create.multiple.stripplots: Added 'type' parameter to allow users to change the type of plotting characters
+* create.heatmap: Added 'xlab' and 'ylab' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.8.1 2011-06-22
+
+MINOR UPDATES
+* create.heatmap: Added functionality of removing column and/or row grid-lines
+* Updated package dependency versions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.8.0 2011-06-17
+
+MAJOR UPDATES
+* create.multiple.stripplots: Added new plotting function to create multiple stripplots
+
+MINOR UPDATES:
+* create.multiple.boxplots: Added 'header.cex' parameter to control font size of the header
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.7 2011-06-16
+
+MINOR UPDATES
+* create.violin.plot: Added 'xaxis.labels' and 'yaxis.labels' parameters to control axes labelling
+* create.heatmap: Added 'top.padding' and 'bottom.padding' parameters to control top and bottom margins
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.6 2011-06-08
+
+MINOR UPDATES
+* Updated plotting functions for NAMESPACE
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.5 2011-06-08
+
+MINOR UPDATES
+* create.histogram: Added 'lwd' and 'lty' parameters to control line width and line style
+* create.histogram: Fixed code to work without axes labels
+* create.scatterplot: Added 'lty' parameter to control line style and adjusted example
+* create.scatterplot.with.error: Added 'lty' parameter and adjusted example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.4 2011-06-07
+
+MINOR UPDATES
+* Added NAMESPACE
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.3 2011-05-31
+
+MINOR UPDATES
+* get.corr.key: Fixed syntax error in example
+* create.boxplot: Reverted functionality to use panel.BL.bwplot
+* create.scatterplot: Updated examples
+* create.histogram: Updated examples
+* create.scatterplot.with.error: Updated examples
+* create.violinplot: Updated examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.2 2011-05-19
+
+MINOR UPDATES
+* create.heatmap: Added 'right.padding' and 'left.padding' parameters to control margins
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.1 2011-05-17
+
+MINOR UPDATES
+* get.corr.key: Cleaned code
+* create.hexbinplot: Cleaned code and fixed links in documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.7.0 2011-05-12
+
+BUG FIXES
+* create.hexbinplot: Changed implementation to address critical issues related to 'maxcnt' argument
+
+MINOR UPDATES:
+* create.hexbinplot: Updated documentation with links and example
+* create.barplot: Updated example
+* create.densityplot: Updated example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.7 2011-05-11
+
+MINOR UPDATES
+* get.corr.key: Added 'alpha.background' parameter
+* create.hexbinplot: Development version - bug related to 'maxcnt' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.6 2011-05-02
+
+MINOR UPDATES
+* get.corr.key: Fixed error
+* create.hexbinplot: Added 'grid' and 'abline' parameters and corresponding example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.5 2011-05-02
+
+MINOR UPDATES
+* create.hexbinplot: Added 'colorcut', 'mincnt', 'maxcnt' parameters to allow user to specify number of bins in plot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.4 2011-04-28
+
+MINOR UPDATES
+* get.corr.key: Improved code formatting
+* get.corr.key: Added 'beta0' and 'beta1' options to the key
+* create.hexbinplot: Added 'aspect' parameter to adjust plot size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.3 2011-04-21
+
+MINOR UPDATES
+* create.hexbinplot: Added 'xaxis.cex' and 'yaxis.cex' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.2 2011-04-04
+
+MINOR UPDATES
+* create.boxplot: Updated code to remove unnecessary dependencies
+* create.boxplot: Added 'fill' parameter to control the fill colour and corresponding example
+* create.scatterplot: Updates to the examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.1 2011-04-01
+
+MINOR UPDATES
+* create.dotmap: Reintroduced 'key' parameter into function
+* create.dotmap: Added 'legend' parameter to allow for multiple keys
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.6.0 2011-03-13
+
+MAJOR UPDATES
+* create.scatterplot: Updated functionality to allow for log-scale x- and y-axes
+
+MINOR UPDATES
+* create.scatterplot: Cleaned up documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.7 2011-03-11
+
+MINOR UPDATES
+* create.densityplot: Added 'xaxis.labels' and 'yaxis.labels' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.6 2011-03-10
+
+MINOR UPDATES
+* create.violin.plot: Added example using legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.5 2011-03-10
+
+MINOR UPDATES
+* create.scatterplot.with.error: Added example using legend
+* create.scatterplot: Updated example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.4 2011-03-10
+
+MINOR UPDATES
+* create.hexbinplot: Added example using legend
+* create.histogram: Added example using legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.3 2011-03-10
+
+MINOR UPDATES
+* create.boxplot: Added example using legend
+* create.densityplot: Added example using legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.2 2011-03-10
+
+MINOR UPDATES
+* create.barplot.with.error: Added example using legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.1 2011-03-10
+
+MINOR UPDATES
+* create.barplot: Added example using legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.5.0 2011-03-09
+
+MINOR UPDATES
+* create.barplot.with.error: Updated example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.4.0 2011-03-08
+
+MINOR UPDATES
+* create.dotmap: Removed 'legend' parameter
+* create.scatterplot: Updated example filenames
+* create.scatterplot: Added example using legend
+* create.barplot.with.error: Cleaned up code
+* create.densityplot: Updated code to use a single panel function
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.3.3 2011-03-03
+
+MINOR UPDATES
+* create.heatmap: Updated examples to be sequential and added example using covariates
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.3.2 2011-02-23
+
+MINOR UPDATES
+* create.scatterplot: Added 'abline' argument
+* create.scatterplot.with.error: Added 'abline' argument
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.3.1 2011-02-23
+
+MINOR UPDATES
+* create.scatterplot: Added ability to add multiple keys to a single plot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.3.0 2011-02-22
+
+MINOR UPDATES
+* create.scatterplot: Cleaned up code to use a single panel function
+* create.scatterplot.with.error: Cleaned up code to use a single panel function
+* create.scatterplot.with.error: Updated formatting to use tabs instead of spaces
+* create.scatterplot.with.error: Cleaned up documentation and examples
+
+BUG FIXES
+* create.scatterplot.with.error: Fixed bug that prevented keys from being plotted
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.2.0 2011-02-22
+
+MINOR UPDATES
+* create.densityplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
+* create.scatterplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
+* create.scatterplot.with.error: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.1.0 2011-02-22
+
+MAJOR UPDATES
+* Added 'legend' and 'key' parameters to plotting functions
+
+MINOR UPDATES
+* create.scatterplot: Added example using a legend
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.24 2011-02-21
+
+BUG FIXES
+* get.corr.key: Fixed bug related to using phantom instead of phantom(0)
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.23 2011-02-19
+
+MINOR UPDATES
+* create.barplot: Updated to allow use of non-factorial variables for grouping
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.22 2011-02-17
+
+BUG FIXES
+* create.scatterplot.with.error: Fixed error related to grid
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.21 2011-02-14
+
+BUG FIXES
+* create.scatterplot: Fixed error related to 'ylimits' and 'xlimits', 'yat' and 'xat
+* create.scatterplot.with.error: Fixed error related to grouped line graphs
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.20 2011-02-13
+
+MINOR UPDATES
+* create.barplot: Changed to prevent spurious warnings when specifying colours with ungrouped data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.19 2011-02-11
+
+MINOR UPDATES
+* create.heatmap: Updated examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.18 2011-02-11
+
+MINOR UPDATES
+* create.heatmap: Cleaned up code to remove deprecated parameter 'colour.number.tweak'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.17 2011-02-09
+
+MINOR UPDATES
+* create.scatterplot: Cleaned up examples to all use the same dataset
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.16 2011-02-07
+
+MINOR UPDATES
+* create.scatterplot.with.error: Cleaned up code to match documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.15 2011-02-04
+
+MINOR UPDATES
+* generate.at.final: Added function to add tick marks to plots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.14 2011-01-31
+
+MINOR UPDATES
+* get.corr.key: Added documentation to function for automatically generating a legend with correlation, beta, and p-values
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.13 2011-01-31
+
+MINOR UPDATES
+* get.corr.key: Updated to code
+* Updated required packages
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.12 2011-01-25
+
+MINOR UPDATES
+* generate.at.final: Added documentation
+* get.corr.key: Added option of including beta
+
+BUG FIXES
+* create.densityplot: Addressed problem of grid drawing and tick mark locations not lining up when both are required - this achieved by removing default grid lines and redrawing them using panel.abline() at user-specified locations
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.11 2011-01-17
+
+MINOR UPDATES
+* get.corr.key: Added flexibility to have rho in Greek
+* write.plot: Added functionality to call CairoTIFF if default tiff has problems
+* create.dotmap: Updated default value of 'xaxis.lab' and 'yaxis.lab' to NULL in order to accept expressions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.10 2011-01-07
+
+MINOR UPDATES
+* get.corr.key: Added function to add basic correlation key to scatter-like plots
+* create.barplot: Updated documentation and examples to use more complex datasets and demonstrate use of 'ylim' and 'yat' parameters
+* create.barplot: Added 'key' parameter
+* create.barplot: Changed 'groups' parameter to accept an expression or variable
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.9 2010-12-22
+
+MINOR UPDATES
+* create.barplot: Added filename to stacked barplot examples
+
+BUG FIXES
+* create.barplot: Fixed problem with groups
+* create.barplot.with.error: Fixed problem with groups
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.8 2010-12-21
+
+MINOR UPDATES
+* create.barplot: Added user-control for colour picking for groups
+* create.barplot.with.error: Added user-control for colour picking for groups
+* create.barplot: Added 'group' and 'stack' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.7 2010-11-29
+
+MINOR UPDATES
+* create.scatterplot: Added ability to rotate text in axis labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.6 2010-11-17
+
+MINOR UPDATES
+* create.scatterplot.with.error: Added group-specific error bar colour handling under no conditioning
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.5 2010-11-17
+
+MINOR UPDATES
+* create.scatterplot.with.error: Added 'add.axes' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.4 2010-11-16
+
+MINOR UPDATES
+* create.scatterplot.with.error: Added ability to handle grouped data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.3 2010-11-15
+
+MINOR UPDATES
+* create.scatterplot: Added 'xaxis.labels' and 'yaxis.labels' parameter to allow customization of axis labels
+* get.defaults: Updated to handle font changes with R v2.12.0
+* create.dotmap: Updated examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.2 2010-11-15
+
+MINOR UPDATES
+* create.scatterplot: Added ability to handle grouped data
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.1 2010-11-11
+
+MINOR UPDATES
+* Updated platform-specific code to work better with changes in R v2.12.0
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 2.0.0 2010-11-02
+
+MAJOR UPDATES
+* Updated package dependencies
+* Updated all plotting functions to take a main title
+* get.defaults: Fixed bug related to changes in newest versions of R and lattice
+* create.heatmap: Updated colouring functionality to reduce possibility of error
+* create.histogram: Added functionality of colouring bars
+* create.hexbinplot: Added functionality of specifying label sizes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.11.2 2010-10-26
+
+MINOR UPDATES
+* create.boxplot: Added 'lwd' parameter to support production of smaller images
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.11.1 2010-10-20
+
+MINOR UPDATES
+* create.boxplot: Updated to facilitate horizontal boxplots annotations for x-axis
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.11.0 2010-10-14
+
+MAJOR UPDATES
+* write.plot: Added new function to standardize plotting output - now used in all plotting functions
+
+MINOR UPDATES
+* create.barplot.with.error: Changed default line width of bar outline to match line width of error bar
+* create.barplot: Updated layout of figure to match other plotting functions
+* Removed 'compression' parameter from plotting functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.10.1 2010-09-23
+
+MINOR UPDATES
+* create.multiple.boxplots: Reordered parameters to be consisting with other plotting functions
+* create.multiple.boxplots: Added 'symbol.cex' parameter to control size of boxplot dots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.10.0 2010-09-22
+
+BUG FIXES
+* create.boxplot: Fixed so that 'ylimits' argument is no longer silently ignored
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.21 2010-09-16
+
+MINOR UPDATES
+* create.violin.plot: Updated documentation to clarify circumstances when 'x' will be coerced to a factor or shingle (when horizontal argument set to FALSE)
+* create.hexbinplot: Added 'compression' and 'add.axes' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.20 2010-09-15
+
+MINOR UPDATES
+* create.multiple.boxplots: Updated 'right.padding' to be set to 2
+* create.barplot.with.error: Renamed function from create.barplot.with.error.r into create.barplot.with.error.R
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.19 2010-09-12
+
+MINOR UPDATES
+* Updated documentation of plotting functions
+* Updated plotting functions to output a trellis object by default
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.18 2010-09-03
+
+BUG FIXES
+* create.barplot: Fixed bug that prevented implicit grouping from working
+* create.barplot.with.error: Fixed bug that prevented implicit grouping from working
+* create.scatterplot.with.error: Fixed bug that prevented implicit grouping from working
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.17 2010-08-31
+
+BUG FIXES
+* create.scatterplot: Fixed bug that prevented implicit grouping from working
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.16 2010-08-27
+
+MINOR UPDATES
+* create.barplot.with.error: Added function to create barplots with customizable error bars
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.15 2010-08-26
+
+MINOR UPDATES
+* create.violinplot: Added 'horizontal' parameter to allow user to specify whether to plot horizontally or vertically
+* create.scatterplot.with.error: Added 'y.error.up', 'y.error.down', 'x.error.right', 'x.error.left' parameter to allow for drawing horizontal and/or vertical error bars (removed 'error.plus' and 'error.minus' parameters)
+* create.scatterplot.with.error: Added 'x.error.bar.col' and 'y.error.bar.col' parameters
+* create.scatterplot.with.error: Added 'error.whisker.angle' parameter to control the angle of whiskers drawn at both ends of the error bars
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.14 2010-08-19
+
+MINOR UPDATES
+* create.boxplot: Added 'xaxis.labels' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.13 2010-08-15
+
+MINOR UPDATES
+* Added warnings framework to plotting functions
+* Updated functions to correctly deal with postscript graphics device
+* Reimplemented fonts mechanism to support Win/*Nix systems correctly w.r.t postscript specific exceptions
+* create.heatmap: Added 'cor.method' parameter
+
+BUG FIXES
+* panel.BL.bwplot: Fixed function to show outlier points properly when input argument box.colour is a vector
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.12 2010-08-07
+
+MINOR UPDATES
+* create.barplot: Updated default to give x-axis and y-axis scale labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.11 2010-08-07
+
+MINOR UPDATES
+* Updated plotting functions to offer OS specific settings framework
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.10 2010-08-07
+
+MINOR UPDATES
+* Updated plotting function documentation with "See Also" links and standardizations to the "Value" section
+* create.heatmap: Renamed 'legend.cex' parameter to 'colorkey.cex'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.9 2010-08-06
+
+MINOR UPDATES
+* Updated plotting functions to have the same default font type
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.8 2010-08-05
+
+BUG FIXES:
+* create.heatmap: Fixed functionality of 'colour.alpha' parameter
+
+MINOR UPDATES
+* create.heatmap: Added example to demonstrate usage of 'colour.alpha' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.7 2010-08-04
+
+MINOR UPDATES
+* create.scatterplot.with.error: Added function to create scatterplot with error bars overlaid
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.6 2010-08-04
+
+MINOR UPDATES
+* create.barplot: Added 'yaxis.labels' parameter
+* create.scatterplot: Changed panel function to allow for update() to change conditioned trellis object
+* create.multiple.boxplots: Changed c() to stack() to accommodate data.frames
+* create.violin.plot: Updated to match other plotting functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.5 2010-07-29
+
+MINOR UPDATES
+* create.barplot: Added 'col' parameter to control the fill colour of bars
+* create.scatterplot: Added default values for some parameters
+* create.stripplot: Added default values for some parameters
+* create.violinplot: Added default values for some parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.4 2010-07-26
+
+MINOR UPDATES
+* create.barplot: Renamed parameters to standardize with other plotting functions
+* create.multiple.boxplots: Renamed parameters to standardize with other plotting functions
+* create.heatmap: Added verbose warning when function cannot generate a figure
+* create.boxplot: Fixed broken default handling of y-axis scale labels
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.3 2010-06-29
+
+BUG FIXES
+* create.heatmap: Fixed bug to accept NAs when specifying colour-ranges
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.2 2010-06-28
+
+MINOR UPDATES
+* create.barplot: Changed 'xlab' and 'ylab' parameters into 'xlab.label' and 'ylab.label' and reordered parameters
+* create.boxplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', and 'ylabel.cex' parameters into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
+* create.hexbinplot: Changed 'xlabel', 'ylabel' parameters into 'xlab.label', 'ylab.label'
+* create.stripplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
+* create.violinplot: Changed 'ylabel' parameter into 'ylab.label'
+* create.histogram: Adjusted example
+* create.multiple.boxplots: Adjusted example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.1 2010-06-25
+
+MINOR UPDATES
+* create.scatterplot: Renamed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' parameters to 'xlab.label', 'ylab.label', 'xlab.cex', 'ylab.cex'
+* create.histogram: Changed default to plot percentages instead of densities
+* create.scatterplot: Adjusted example to show extra features
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.9.0 2010-06-24
+
+MAJOR UPDATES
+* create.densityplot: Added new function to plot densities
+
+MINOR UPDATES
+* create.histogram: Added many new parameters, changed order of parameters, renamed parameters for standardization
+* create.boxplot: Improved example
+* create.histogram: Improved example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.8.1 2010-06-24
+
+MINOR UPDATES
+* Updated parameter ordering of plotting functions to bring 'filename' parameter to the front of each function, and the height, width, and resolution parameters to the back
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.8.0 2010-06-24
+
+MAJOR UPDATES
+* Updated plotting functions to return the trellis object only if filename = NULL
+* All example files are named after the method that produced them
+* Standardized variable names of plotting objects to trellis.object
+
+MINOR UPDATES
+* create.multiple.boxplots: Fixed spacing/indentation to match coding standard
+* create.histogram: Reordered parameters to have mandatory parameters come first
+* create.stripplot: Reordered parameters to have mandatory parameters come first
+* create.violinplot: Reordered parameters to have mandatory parameters come first
+* create.histogram: Allowed lattice default values for breaks, ylimits, etc
+* create.violinplot: Allowed lattice default values for ylimits, yat
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.7.3 2010-06-23
+
+MINOR UPDATES
+* create.heatmap: Added examples to documentation
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.7.2 2010-06-22
+
+BUG FIXES
+* create.heatmap: Fixed but in example by changing dataset
+* scientific.notation.2: Fixed function to display the last digit as 0 when requested
+
+MINOR UPDATES
+* create.heatmap: Added 'colorkey.labels' parameter
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.7.1 2010-06-15
+
+MINOR UPDATES
+* create.boxplot: Renamed parameter 'ylimit' to 'ylimits' to standardize with other plotting functions
+* Updates to documentation and code formatting for standardization
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.7.0 2010-06-13
+
+MAJOR UPDATES
+* Propagated graphics device changes to all plotting functions - enforced graphics type to 'cairo'
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.27 2010-06-11
+
+MINOR UPDATES
+* create.heatmap: Added 'at' and 'colorkey.labels.at' parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.26 2010-06-07
+
+MINOR UPDATES
+* create.heatmap: Enforced graphics type to 'cairo' for all platforms
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.25 2010-06-02
+
+MINOR UPDATES
+* panel.BL.bwplot: Updated documentation
+* create.scatterplot: Renamed 'lwdoutline' parameter to 'axis.lwd' for consistency in parameter names
+* create.scatterplot: Added parameters for fontfaces of x- and y-axis scales
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.24 2010-06-02
+
+MINOR UPDATES
+* create.scatterplot: Updated to allow alteration of more plotting parameters and to match other plotting functions
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.23 2010-06-01
+
+MINOR UPDATES
+* create.stripplot: Updated to allow for alteration of more plotting parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.22 2010-05-27
+
+MINOR UPDATES
+* create.boxplot: Updated to allow for alteration of more plotting parameters
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.21 2010-05-26
+
+MINOR UPDATES
+* create.heatmap: Changed default colour.scheme from legacy parameter-handling
+* create.heatmap: Removed spurious warnings in legacy code and added error-handling for bad usage
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.20 2010-05-26
+
+MINOR UPDATES
+* create.scatterplot: Added 'compression' parameter for tiff file customization
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.19 2010-05-25
+
+MINOR UPDATES
+* create.heatmap: Allowed clustering of only one dimension at a time
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.18 2010-04-26
+
+MINOR UPDATES
+* create.scatterplot: Added 'lwd' parameter for best-fit lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.17 2010-04-24
+
+MINOR UPDATES
+* create.heatmap: Changed ordering of top covariates to match right covariates
+* create.heatmap: Changed axis tick-marks to be dynamic based on number of rows/columns in the heatmap
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.16 2010-04-23
+
+MINOR UPDATES
+* create.scatterplot: Allowed for removal of axis-lines
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.15 2010-04-14
+
+BUG FIXES
+* create.boxplot: Fixed colouring issues that arose when 'box.colour' argument was passed as a vector
+
+MINOR UPDATES
+* panel.BL.bwplot: Added this function to fix colouring issues with lattice::panel.bwplot()
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.14 2010-04-12
+
+MINOR UPDATES
+* create.heatmap: Added 'fill.colour' parameter for background
+* create.heatmap: Allowed specification of arbitrary colour-combinations
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.13 2010-04-11
+
+MINOR UPDATES
+* create.heatmap: Added parameter for covariate-size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.12 2010-04-09
+
+MINOR UPDATES
+* create.heatmap: Allowed for plotting of arbitrarily large heatmaps when clustering is turned off
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.11 2010-04-09
+
+MINOR UPDATES
+* create.boxplot: Removed pass-through parameterization because it can cause crashes when a fixed parameter is duplicated
+* create.boxplot: Allowed separate sizing of axis labels and axis scales
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.10 2010-04-02
+
+MINOR UPDATES
+* create.boxplot: Renamed 'box.color' to 'box.colour' to match other variables
+* create.boxplot: Added 'symbol.cex' parameter to adjust outlier point size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.9 2010-04-01
+
+MINOR UPDATES
+* create.barplot: Parameterized label-sizes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.8 2010-04-01
+
+MINOR UPDATES
+* create.boxplot: Added 'box.color' parameter
+* create.boxplot: Updated to return a handle to plot object and added default values to input arguments
+* create.multiple.boxplots: Updated to get better memory efficiency
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.7 2010-03-31
+
+MINOR UPDATES
+* create.barplot: Adjusted cex parameters
+* create.histogram: Updated to allow specification of type (percent, count, or density)
+* Cleaned up documentation to reduce warnings and be more explicit
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.6 2010-03-24
+
+MINOR UPDATES
+* scientific.notation.2: Updated to allow proper handling of zeros
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.5 2010-03-15
+
+MINOR UPDATES
+* create.heatmap: Updated to allow for adjustment of colour-range
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.4 2010-03-14
+
+MINOR UPDATES
+* create.heatmap: Added selective plotting of right/top/left dendrograms
+* create.heatmap: Improved colour-palette selection by calculating the range of the data
+* create.heatmap: Allowed specification of main figure title
+* create.heatmap: Allowed separate output of a file and/or return of a trellis object
+* Enforced minimum version numbers on package dependencies
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.3 2010-03-14
+
+MINOR UPDATES
+* create.heatmap: Added BlueWhiteYellow colour-scheme
+* create.heatmap: Updated to not run wit an invalid colour-scheme
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.2 2010-03-05
+
+MINOR UPDATES
+* create.boxplot: Added option to plot or not plot outliers
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.6.1 2010-03-03
+
+MINOR UPDATES
+* create.hexbinplot: Added new function to create hexbin plots
+* create.boxplot: Updated to control x- and y-axis tick sizes
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.5.3 2010-03-01
+
+MINOR UPDATES
+* create.heatmap: Added ability to change legend size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.5.2 2010-02-26
+
+MINOR UPDATES
+* create.boxplot: Updated so that x-axis label does not overlap with x-axis ticks
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.5.1 2010-02-26
+
+MINOR UPDATES
+* create.boxplot: Updated to be able to set label size
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.5.0 2010-02-25
+
+MAJOR UPDATES
+* create.dotmap: Added new function to create dotmaps
+
+MINOR UPDATES
+* create.scatterplot: Added examples
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.12 2010-02-24
+
+MINOR UPDATES
+* create.scatterplot: Added parameters for plot-type, point/line size, colour, and symbol
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.11 2010-02-19
+
+MINOR UPDATES
+* create.barplot: Fixed handling of clustering methods other than 'none' or 'diana'
+* create.heatmap: Allowed for column-wise covariates
+* create.heatmap: Allowed for any agglomerative clustering method available via hclust
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.10 2010-02-08
+
+MINOR UPDATES
+* create.boxplot: Allowed for rotation of x-axis names
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.9 2010-02-06
+
+MINOR UPDATES
+* create.stripplot: Added new function to create strip plot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.8 2010-02-03
+
+MINOR UPDATES
+* create.barplot: Added new function to create barplot
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.7 2010-02-01
+
+MINOR UPDATES
+* create.boxplot: Updated to save figure directly and added example
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.6 2010-01-29
+
+BUG FIXES
+* create.heatmap: Fixed bug in parameter-handling that introduced spurious warnings
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.5 2010-01-29
+
+MINOR UPDATES
+* create.multiple.boxplots: Modified to remove build/check warnings
+* create.multiple.boxplots: Modified to ensure functionality when 'plot.names' input has less components than the 'data' input
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.4 2010-01-29
+
+BUG FIXES
+* create.multiple.boxplots: Fixed error where \usage called wrong function name and one argument was missing in \arguments
+
+MAJOR UPDATES
+* create.boxplot: Added new function to create boxplots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.3 2010-01-28
+
+MAJOR UPDATES
+* create.multiple.boxplots: Added new function to create multiple boxplots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.2 2010-01-27
+
+MINOR UPDATES
+* create.heatmap: Added ability to have clustered data without dendrograms
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.1 2010-01-27
+
+MINOR UPDATES
+* create.heatmap: Added ability to handle different clustering algorithms and not plot dendrograms
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.4.0 2010-01-27
+
+MAJOR UPDATES
+* create.histogram: Added function to create histograms
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.3.0 2010-01-26
+
+MAJOR UPDATES
+* create.scatterplot: Added function to create scatterplots
+* scientific.notation.2: Added function to facilitate embedding of scientific notation inside other figures
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.2.0 2010-01-07
+
+MAJOR UPDATES
+* scientific.notation: Added function to allow for proper scientific notation in plots
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.1.0 2010-01-07
+
+MAJOR UPDATES
+* create.heatmap: Added function to create heatmaps
+---------------------------------------------------------------------------------------------------
+BoutrosLab.plotting.general 1.0.0 2010-01-06
+
+MAJOR UPDATES
+* Initialized package for plotting functions
+* create.violin.plot: Added function to create violin plots
+---------------------------------------------------------------------------------------------------
+
+
diff --git a/NEWS.md b/NEWS.md
index c271db6..9389296 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 - Improved "sample.order" argument checking
 - Updated NEWS to Markdown NEWS.md format
+- Cleaned the C++ namespace by using `R_` versions of Free, Calloc, and Realloc
 
 # BoutrosLab.plotting.general 7.1.1 (2024-01-08)
 
diff --git a/src/ks.c b/src/ks.c
index 15d2a4e..27063e0 100644
--- a/src/ks.c
+++ b/src/ks.c
@@ -148,8 +148,8 @@ K(int n, double d)
    k = (int) (n * d) + 1;
    m = 2 * k - 1;
    h = k - n * d;
-   H = (double*) Calloc(m * m, double);
-   Q = (double*) Calloc(m * m, double);
+   H = (double*) R_Calloc(m * m, double);
+   Q = (double*) R_Calloc(m * m, double);
    for(i = 0; i < m; i++)
        for(j = 0; j < m; j++)
 	   if(i - j + 1 < 0)
@@ -177,8 +177,8 @@ K(int n, double d)
        }
    }
    s *= pow(10., eQ);
-   Free(H);
-   Free(Q);
+   R_Free(H);
+   R_Free(Q);
    return(s);
 }
 
@@ -215,7 +215,7 @@ m_power(double *A, int eA, double *V, int *eV, int m, int n)
 	return;
     }
     m_power(A, eA, V, eV, m, n / 2);
-    B = (double*) Calloc(m * m, double);
+    B = (double*) R_Calloc(m * m, double);
     m_multiply(V, V, B, m);
     eB = 2 * (*eV);
     if((n % 2) == 0) {
@@ -232,7 +232,7 @@ m_power(double *A, int eA, double *V, int *eV, int m, int n)
 	    V[i] = V[i] * 1e-140;
 	*eV += 140;
     }
-    Free(B);
+    R_Free(B);
 }
 
 /* Two-sided two-sample */