ggpubr 0.6.0

New features

• New function ggadjust_pvalue() added to adjust p-values produced by geom_pwc() on a ggplot (#522).
• New data added: gene_expression
• Global options: New available package options: ggpubr.null_device, which value should be a function that creates an appropriate null device. These include: cowplot::pdf_null_device, cowplot::png_null_device, cowplot::cairo_null_device and cowplot::agg_null_device. Default is cowplot::pdf_null_device. This is used in function like as_ggplot(), which needs to open a graphics device to render ggplot objects into grid graphics objects. This function is used to open null device for avoiding the display of unnecessary blank page when calling ggarrange() or as_ggplot() (#306 and #158). The default option can be changed using, for example, options(ggpubr.null_device = cowplot::png_null_device).

Major changes

• gadd(): Restoring back random state after setting seed when adding jittered points. To do so, the seed number is just passed to position_jitter() and position_jitterdodge(), which preserve the initial random state ( #177 and #349) .
• ggpubr requires now a version of ggrepel >= 0.9.2.9999, which restores now the initial random state after set.seed(). see slowkow/ggrepel#228
• ggpubr requires now a version of cowplot >= 1.1.1

Minor changes

• ggtexttable(): doc updated with another example; text justification for individual cells/rows/columns (#335).
• ggpie(): setting the default of clip = "off" in coord_polar() so that ggpie() does not crop labels (#429)
• as_ggplot(): using null_device to avoid blank page #306 and #158
• ggarrange(): using null_device to avoid blank page #306 and #158
• Indexing variable in a data frame: using df[[x]] instead of df[, x] to make sure that the result is a vector even if the df is a tibble.
• ggexport(): support added for graphics device svg (#469)
• ggpie() and ggdonutchart() now fully reacts to the option lab.font (#502)
• Replacing deprecated gather_() in both internal (.check_data()) and exported functions (compare_means()) (#513)
• stat_compare_means(): The dot-dot notation (..p.signif..) was deprecated in ggplot2 3.4.0; after_stat(p.signif) should be used; updated so that ..p.signif.. is automatically converted into after_stat() format without warning for bacward compatibility.
• Enable faceting by column names with spaces (#391)
• Licence changed to GPL (>= 2) (#482)
• desc_statby() doc updated to clarify the difference between SD (standard deviation) and SE (standard error) (#492)
• The message geom_smooth() using formula 'y ~ x' is now turned off in ggscatter()(#488)

Bug fixes

• ggtext(): fix warning "filter_() was deprecated in dplyr 0.7.0".
• ggqqplot(): the argument conf.int is taken into account now when specified (#524).
• ggqqplot(): Fixing the warning: "The following aesthetics were dropped during statistical transformation: sample" (#523)
• Requiring rstatix v >=0.7.1.999 for preserving factor class in emmeans_test() (#386)
• ggmaplot(): Suppressing ggmaplot warning: Unlabeled data points (too many overlaps). Consider increasing max.overlaps (#520)
• compare_means(): works now when the grouping variable levels contain the key words group2 or group1 (#450)
• ggparagraph() : fixing bug about minimum paragraph length (#408)
• ggexport(): the verbose argument is now considered when specifyed by user (#474)

ggpubr 0.5.0

New features

• New functions stat_anova_test(), stat_kruskal_test(), stat_welch_anova_test(), stat_friedman_test() and geom_pwc() added. These are flexible functions to add p-values onto ggplot with more options. The function geom_pwc() is for adding pairwise comparisons p-values to a ggplot; supportted statistical methods include "wilcox_test", "t_test", "sign_test", "dunn_test", "emmeans_test", "tukey_hsd" and "games_howell_test".
• New functions to convert character vector coordinates into NPC (normalized parent coordinates) and data coordinates: as_npc(), npc_to_data_coordinates() and get_coord().
• Global options:
  • New function ggpubr_options() to display allowed global options in ggpubr
  • New available package options: ggpubr.parse_aes. logical indicating whether to parse or not the aesthetics variables names. Default is TRUE. For example, if you want ggpubr to handle non-standard column names, like A-A, without parsing, then set this option to FALSE using options(ggpubr.parse_aes = FALSE).

Minor changes

• Minimum rstatix version needed is set to 0.7.1
• Minimum ggplot2 version needed is set to 3.4.0
• stat_conf_ellipse: ensure stat returns a data.frame for compatibility with ggplot2 v>=3.4.0
• stat_compare_means():
  • Unit tests added
  • Updated to use after_stat(p.signif) as the dot-dot notation (..p.signif..) was deprecated in ggplot2 3.4.0 (#509).
• ggdensity() and gghistogram(): dot-dot notation (..density.., ..count..) replaced by after_stat(density) and after_stat(count), respectively for compatibility with ggplot2 3.4.0.
• create_aes():
  • Default is now to parse its input, which can be an expression (#348). If you want ggpubr to handle non-standard column names (#229), like A-A, without parsing, then set this option to FALSE using options(ggpubr.parse_aes = FALSE).
  • Supports space in column names like "Dimension 1"
  • Unittest added
• Arguments (digits and table.font.size) added to ggsummarystats() for changing the summary table decimal place and text size (#341).
• In stat_pvalue_manual() the argument hide.ns can be either a logical value (TRUE or FALSE) or a character value ("p" or "p.adj" for filtering out non significant by p-value or adjusted p-values).
• Now, the x-axis tick label names correctly align with the corresponding ticks when the rotation angle of the texts is set to 90. This is automatically achieved by setting internally vjust = 0.5 (#301).
• Capital NS. is no longer displayed by stat_compare_means() (#171)
• Unit tests added forggshistogram() to make sure that it works when:
  • using after_stat(),
  • using after_stat() with trailing space inside parentheses.
• Unit tests added forggscatter() to make sure that:
  • it works when there is spaces in variable names
  • it can handle non-standard column names when ggpubr.parse_aes global option is set to FALSE (#229)

ggpubr 0.4.0

New features

• New functions added to customize ggtexttable() (#125, #129 and #283):
  • tab_cell_crossout(): cross out a table cell.
  • tab_ncol(), tab_nrow(): returns, respectively, the number of columns and rows in a ggtexttable.
  • tab_add_hline(): Creates horizontal lines or separators at the top or the bottom side of a given specified row.
  • tab_add_vline(): Creates vertical lines or separators at the right or the left side of a given specified column.
  • tab_add_border(), tbody_add_border(), thead_add_border(): Add borders to table; tbody is for table body and thead is for table head.
  • tab_add_title() and tab_add_footnote() to add titles and footnotes (#243).
• ggpubr functions updated to handle non-standard column names, for example ("A-A") (#229).
• New function create_aes() added to create aes mapping from a list. Makes programming easy with ggplot2 (#229).
• New argument coord.flip added to support adding p-values onto horizontal ggplots (#179). When adding the p-values to a horizontal ggplot (generated using coord_flip()), you need to specify the option coord.flip = TRUE.
• New errorbar functions - median_hilow_() and median_q1q3() - added (@davidlorenz, #209):
  • median_hilow_(): computes the sample median and a selected pair of outer quantiles having equal tail areas. This function is a reformatted version of Hmisc::smedian.hilow(). The confidence limits are computed as follow: lower.limits = (1-ci)/2 percentiles; upper.limits = (1+ci)/2 percentiles. By default (ci = 0.95), the 2.5th and the 97.5th percentiles are used as the lower and the upper confidence limits, respectively. If you want to use the 25th and the 75th percentiles as the confidence limits, then specify ci = 0.5 or use the function median_q1q3().
  • median_q1q3(): computes the sample median and, the 25th and 75th percentiles. Wrapper around the function median_hilow_() using ci = 0.5.
• New function get_breaks() added to easily create breaks for numeric axes. Can be used to increase the number of x and y ticks by specifying the option n. It's also possible to control axis breaks by specifying a step between ticks. For example, if by = 5, a tick mark is shown on every 5 (@Chitanda-Satou, #258).

Major changes

• The following enhancement has been added to ggscatterhist() (@juliechevalier, #176):
  • the output of ggscatterhist() is now a list of ggplots, containing the main scatter plot (sp) and the marginal plots (xplot and yplot), which can be customized by the end user using the standard ggplot verbs
  • An S3 printing method is now available for an object of class ggscatterhist. The printing method displays the arranged final figure.

Minor changes

• Now, when creating a box plot with error bars, color and fill argiments are taken into account in the errorbar function (#105).
• New argument alternative supported in stat_cor() (#276).
• New argument position in ggline() to make position "dodged" (#52).
• New argument outlier.shape in ggboxplot(). Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.
• Sorting can be now disabled in ggdotchart() using the option sorting = "none" (#115, #223).
• New argument weight added in gghistogram() for creating a weighted histogram (#215)
• Now ggscaterhist() takes into account the argument position in margin.params when marginal plot is a histogram (#286).
• ggbarplot() enhanced to better handle the creation of dodged bar plots combined with jitter points (@aherholt, #176)
• New argument bracket.shorten added in stat_pvalue_manual() and geom_bracket(). a small numeric value in [0-1] for shortening the with of bracket (#285).
• New argument bracket.nudge.y added in stat_pvalue_manual() and geom_bracket(). Vertical adjustment to nudge brackets by. Useful to move up or move down the bracket. If positive value, brackets will be moved up; if negative value, brackets are moved down (#281).
• New argument numeric.x.axis added in ggerrorplot(); logical value, If TRUE, x axis will be treated as numeric. Default is FALSE (#280).
• The option width is now considered in ggadd() for plotting error bars (#278).
• New argument linetype in ggpaired().
• geom_exec() used in ggpaired() to add lines between paired points.
• ggmaplot() now supports two input formats (#198):
  1. baseMean | log2FoldChange|padj: Here, we'll use log2(baseMean) as the x-axis variable
  2. baseMeanLog2 | log2FoldChange|padj: here, baseMeanLog2 is assumed to be the mean of logged values; so we'll use it as x-axis variable without any transformation.
• new arguments added in ggmaplot():
  • alpha for controlling point transparency/density (@apcamargo, #152).
  • label.select to select specific genes to show on the plot (@apastore, #70)
• In ggadd() the fill argument is considered for jitter points only when the point shape is in 21:25 (@atakanekiz, #148).
• New argument parse added in ggscatter() and in ggtext(). If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath (#250).
• New argument stroke supported in ggscatter() and in ggline(). Used only for shapes 21-24 to control the thickness of points border (@bioguy2018, #258).
• the stat_cor() function code has been simplified. New arguments p.accuracy and r.accuracy added; a real value specifying the number of decimal places of precision for the p-value and the correlation coefficient, respectively. Default is NULL. Use (e.g.) 0.01 to show 2 decimal places of precision (@garthtarr, #186, @raedevan6, #114, #270).

Bug fixes

• annotate_figure() manual updated to show how to use of superscript/subscript in the axis labels (#165).
• ggtextable() now supports further customization when theme is specified (#283).
• the argument font.family is now correctly handled by ggscatter() (#149)
• ggpar() arguments are correctly applied using ggpie() (#277).
• ggscatter(): When conf.int = FALSE, fill color is set to "lightgray" for the regression line confidence band (@zhan6073, #111).
• Now, gghistogram() supports the paramter yticks.by (@Chitanda-Satou, #258).

ggpubr 0.3.0

New features

• New functions:
  • ggsummarystats() to create a GGPLOT with summary stats table under the plot ( #251).
  • clean_table_theme() to clean the the theme of a table, such as those created by ggsummarytable()
• ggbarplot() now supports stacked barplots with error bars (#245).

Minor changes

• New arguments:
  • vjsut in stat_compare_means() to move the text up or down relative to the bracket.
  • type in geom_bracket() to specify label type. Can be "text" or "expression" (for parsing plotmath expression); #253.
  • labeller to the function facet()
  • position in get_legend() to specify legend position
  • legend.grob in ggarrange() to specify a common legend you want to add onto the combined plot.
• Maintenance adaptation to dplyr new version by removing deprecated functions, such as group_by_, select_, arrange_, etc

Bug fixes

• Now, Barplots are correctly labelled when custom labels are specified by users (@sekharcu, #234)

ggpubr 0.2.5

Minor changes

• New arguments cor.coef.name in the function stat_cor(). Can be one of "R" (pearson coef), "rho" (spearman coef) and "tau" (kendall coef). Uppercase and lowercase are allowed (@andhamel, #216).
• New arguments digits, r.digits, p.digits in the function stat_cor(). Integer indicating the number of decimal places (round) or significant digits (signif) to be used for the correlation coefficient and the p-value (@raedevan6, #216).
• compare_means() adapted to tidyr v>= 1.0.0 by specifying cols in the unnest() function (@Youguang, #216).

ggpubr 0.2.4

Minor change

• unnest adapted to tidyr 1.0.0
• stat_pvalue_manual() can now handle an rstatix test result containing only one group column.

v0.2.3

New features

• New function stat_central_tendency() to add central tendency measures (mean, median, mode) to density and histogram plots
• New function stat_overlay_normal_density() to overlay normal density plot (with the same mean and SD) to the density distribution of 'x'.

Minor changes

• The option exact = FALSE is no longer used when computing correlation in stat_cor() (@tiagochst, #205)

Bug fixes

• ggpie() keeps now the default order of labels (@WortJohn, #203)

ggpubr 0.2.2

New fatures

• New function geom_bracket() for adding brackets with label annotation to a ggplot. Helpers for adding p-value or significance levels to a plot.

Minor changes

• compare_means() has been adapted to tidyr v1.0.0 (@jennybc, #196)
• geom_exec() now handles geom_bracket() arguments
• New arguments vjust, hide.ns, step.increase, step.group.by, color and linetype added in stat_pvalue_manual()
• stat_pvalue_manual() can now guess automatically the significance label column.
• New argument show.legend added to ggadd() and add_summary() functions.

Bug fixes

• Bug fixes in gghistogram(). Works now when the x variable is R keyword, such as var, mean, etc. (#192)
• In ggline(), error bars now react automatically to grouping by line type (#191)

ggpubr 0.2.1

Minor changes

• New arguments step.increase added in stat_compare_means() to avoid overlap between brackets.
• In stat_pvalue_manual() x axis variable is no longer automatically converted into factor. If your x variable is a factor, make sure that it is converted into factor.
• stat_pvalue_manual() can automatically handle the output of rstatix tests
• ggbarplot() and ggviolin() now automatically create error bars by groups when users forget the option add.params = list(group = ) (#183).
• Now, ggarrange() works when either ncol = 1 or nrow = 1 (@GegznaV, #141.
• When method = "wilcox.test", the function compare_means() set automatically the option exact = FALSE. This is no longer the case (@stemicha, #141.
• stat_pvalue_manual() now supports dodged grouped plots (@emcnerny, #104).
• the argument position is now handled by ggdotplot() (@Adam-JJJJJ, #178)

Bug fixes

• Adding points works now for barplots grouped by fill color (@elenichri)
• label.sep argument works now in ggscatter() and stat_cor() (@sbbmu, #150)
• Fix in ggscatter() to avoid freezing when the add argument is incorrect (@atakanekiz, #135).

ggpubr 0.2

Bug fixes

• P-value for multiple comparisons by group (stat_compare_means()) are now correctly displayed (@elisheva100, #135).