Merge pull request #34 from hancockinformatics/devel

Merge Devel 0.99.66
hancockinformatics · Mar 4, 2024 · 4506c6b · 4506c6b
2 parents 1eab3ee + e7bcc6b
commit 4506c6b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ABCindex
 Title: A Shiny app to calculate ABCI for checkerboard assays
-Version: 0.99.63
+Version: 0.99.66
 Authors@R:
   person(given = "Travis",
          family = "Blimkie",

diff --git a/R/1_home.R b/R/1_home.R
@@ -77,16 +77,16 @@ panel_home <- function(id) {
         )"),
 
         HTML(r"(
-          <p class='lead mb-4'>Here you can calculate ABCIs for your
-          checkerboard data and visualize the results in different plots
+          <p class='lead mb-4'>Here you can calculate ABCI values for your
+          checkerboard data, and visualize the results in different plots
           designed to quickly identify promising interactions and favourable
           drug ratios.</p>
         )"),
 
         HTML(r"(
           <p class='lead mb-4'>Click the Get Started button to upload your
-          data. To learn more about how ABCI is calculated, or how to use
-          ABCindex, check the Help pages below. For more information,
+          data. To see how to use ABCindex, or to learn more about how ABCI is
+          calculated, check the Help pages below. For more information,
           including how to cite ABCindex, please refer to the About page.</p>
         )"),
 

diff --git a/R/2_upload.R b/R/2_upload.R
@@ -723,16 +723,16 @@ panel_upload <- function(id) {
           "separate panels in the final plots, while replicates within an ",
           "experiment will be averaged. You can use the link to ",
           actionLink(ns("download_template"), "download a template"),
-          "of the input format. If required, subtract any 'blank' wells ",
-          "before uploading your data."
+          "of the input format you can paste your data into. If required, ",
+          "subtract any 'blank' wells before uploading your data."
         ),
 
         p(
           "Use the link to ",
           actionLink(ns("load_example_data"), "try our example data"),
-          " or check out the ",
+          ", or check out the ",
           actionLink(ns("help_from_upload"), "Help pages"),
-          "to learn more about the data types we support."
+          "to learn more about the data we support."
         ),
 
         fileInput(
@@ -792,8 +792,8 @@ server_upload <- function(id) {
         size = "m",
         easyClose = TRUE,
         p(
-          "The template data can be downloaded as either a '.xlsx' or '.ods' ",
-          "file using the buttons below."
+          "The input template can be downloaded as either an '.xlsx' or ",
+          "'.ods' file using the buttons below."
         ),
         HTML("<img src='help/input_template.png' class='center'>"),
         br(),
@@ -992,7 +992,7 @@ server_upload <- function(id) {
       removeNotification(ns("upload_notification"))
 
       showModal(modalDialog(
-        title = "Perform ABCI calculations: Data normalization",
+        title = "Data normalization for ABCI calculations",
         size = "l",
         p(r"(
           By default, ABCindex will normalize all input data to percentages. If

diff --git a/R/3_results.R b/R/3_results.R
@@ -45,15 +45,15 @@ line_y <- ggplot2::annotate(
 tooltips <- list(
   abci_colours = paste0(
     "Colour palette for the ABCI values, designed to highlight the most ",
-    "relevant differences. Click to see the options."
+    "relevant differences. Click to see the available options."
   ),
   x_axis_title = "Title for the X axis; applies to the entire plot",
   x_axis_digits =
     "Number of decimal places to show for concentrations on the X axis",
   y_axis_title = "Title for the Y axis; applies to the entire plot",
   y_axis_digits =
     "Number of decimal places to show for concentrations on the Y axis",
-  size_legend = "Title of the size legend in dot plots",
+  size_legend = "Title of the dot size legend",
   draw_activity = paste0(
     "Include line(s) to indicate activity thresholds for individual ",
     "treatments (e.g., MIC, MBIC, MBEC). Defaults to ≥50% killing."
@@ -62,28 +62,30 @@ tooltips <- list(
     "Cutoff value for activity threshold lines (0.5 = 50% killing). Applies ",
     "to both X and Y axes."
   ),
-  swap_x_y = "Turn on to swap the values plotted on the X and Y axis",
-  axis_labels =
-    "Across plot panels, should the X and Y axis labels vary or be the same?",
+  swap_x_y = "Turn on to swap the drugs plotted on the X and Y axis",
+  axis_labels = paste0(
+    "Should the X and Y axis labels be drawn on every panel? Turn on when all ",
+    "experiments have the same concentrations."
+  ),
   low_effect = paste0(
-    "Draw a symbol on tiles with low effect when treatments are combined. ",
-    "Defaults to <50% killing."
+    "Draw a symbol on tiles with low effect (<50% killing) when treatments ",
+    "are combined"
   ),
   low_effect_val = paste0(
-    "Draw a symbol on combined treatment cells that kill less than the ",
-    "indicated percentage (0.5 = 50% killing)."
+    "Threshold for drawing a symbol on tiles with low effect when treatments ",
+    "are combined (0.5 = 50% killing)"
   ),
   large_effect = paste0(
     "Outline dots, or draw a symbol on tiles, to highlight combinations with ",
-    "high killing"
+    "high killing (>90% killing)"
   ),
   large_effect_val = paste0(
     "Threshold value used for highlighting combinations with a large effect ",
     "(0.9 = 90% killing)"
   ),
   abci_val = paste0(
     "When highlighting combinations with a large effect, only those with an ",
-    "ABCI value above this number will be included."
+    "ABCI value above this threshold will be included"
   ),
   filter = paste0(
     "Choose whether to include ABCI values close to 0 (Loose) or hide them ",
@@ -92,7 +94,7 @@ tooltips <- list(
   linear = "Toggle to enable linear/continuous scaling for dot sizes",
   zero_lines = paste0(
     "Draw lines inside the plot to distinguish wells without the presence of ",
-    "one compound"
+    "one treatment"
   )
 )
 
@@ -109,13 +111,13 @@ plot_legends <- list(
   dot = div(
     p(
       "This graph combines ABCI (drug interaction) and activity (% killed). ",
-      "The colour of the dots indicates ABCI: Positive ABCI values indicate ",
-      "that the combination is more effective than any individual drug on its ",
-      "own; negative values indicate that the combination is less effective ",
-      "than at least the most active individual drug. The size of the dots ",
-      "indicates the percentage of biomass killed. Vertical and horizontal ",
-      "lines can be added to illustrate the activity thresholds of the ",
-      "individual drugs (e.g. MIC)."
+      "The colour of the dots indicates ABCI: Positive values indicate that ",
+      "the combination is more effective than either individual drug; ",
+      "negative values indicate that the combination is less effective than ",
+      "the most active individual drug. The size of the dots indicates the ",
+      "percentage of biomass killed. Vertical and horizontal lines can be ",
+      "added to illustrate the activity thresholds for the individual drugs ",
+      "(e.g. MIC)."
     ),
     link_paragraph,
     p(
@@ -124,26 +126,26 @@ plot_legends <- list(
       "using the Anti-Biofilm Combination Index (ABCI, colour scale) and ",
       "percentage of [biofilm inhibition], relative to the average of the ",
       "untreated control. Results are the average of [X] replicates. Positive ",
-      "ABCI values indicate a combination more effective than each individual ",
-      "drug, while negative values indicate a combination less effective than ",
-      "at least the most active individual drug; see materials and methods ",
-      "for ABCI calculation. Vertical and horizontal lines indicate the ",
-      "[MBIC50] of individual drugs. Created with ABCindex [Citation]."
+      "ABCI values indicate a combination more effective than the individual ",
+      "drugs, while negative values indicate a combination less effective ",
+      "than the most active individual drug; see materials and methods for ",
+      "ABCI calculation. Vertical and horizontal lines indicate the [MBIC50] ",
+      "of individual drugs. Created with ABCindex [Citation]."
     )
   ),
 
   dot_split = div(
     p(
       "This graph combines ABCI (drug interaction) and activity (% killed). ",
-      "The colour of the dots indicates ABCI: Positive ABCI values (top) ",
-      "indicate that the combination is more effective than any individual ",
-      "drug on its own; negative values (bottom) indicate that the ",
-      "combination is less effective than at least the most active individual ",
-      "drug. They have been split into two different plots for visually ",
-      "simplified illustrations of only positive or negative interactions. ",
-      "The size of the dots indicates the percentage of biomass killed. ",
-      "Vertical and horizontal lines can be added to illustrate the activity ",
-      "thresholds of the individual drugs (e.g. MIC)."
+      "The colour of the dots indicates ABCI: Positive values (top) indicate ",
+      "that the combination is more effective than either individual drug; ",
+      "negative values (bottom) indicate that the combination is less ",
+      "effective than the most active individual drug. They have been split ",
+      "into two different plots for visually simplified illustrations of only ",
+      "positive or negative interactions. The size of the dots indicates the ",
+      "percentage of biomass killed. Vertical and horizontal lines can be ",
+      "added to illustrate the activity thresholds of the individual drugs ",
+      "(e.g. MIC)."
     ),
     link_paragraph,
     p(
@@ -154,46 +156,45 @@ plot_legends <- list(
       "untreated controls. Results are the average of [X] replicates. ",
       "Positive ABCI values (top) indicate a combination more effective than ",
       "each individual drug, while negative values (bottom) indicate a ",
-      "combination less effective than at least the most active individual ",
-      "drug; see materials and methods for ABCI calculation. Vertical and ",
-      "horizontal lines indicate the [MBIC50] of individual drugs. Created ",
-      "with ABCindex [Citation]."
+      "combination less effective than the most active individual drug; see ",
+      "materials and methods for ABCI calculation. Vertical and horizontal ",
+      "lines indicate the [MBIC50] of individual drugs. Created with ABCindex ",
+      "[Citation]."
     )
   ),
 
   tile = div(
     p(
-      "The colour of the tiles indicates ABCI: Positive ABCI values indicate ",
-      "that the combination is more effective than any individual drug on its ",
+      "The colour of the tiles indicates ABCI: Positive values indicate that ",
+      "the combination is more effective than either individual drug on its ",
       "own; negative values indicate that the combination is less effective ",
-      "than at least the most active individual drug. Vertical and horizontal ",
-      "lines can be added to illustrate the activity thresholds of the ",
-      "individual drugs (e.g. MIC). Activity (% killing) is not depicted; ",
-      "combining this with a line plot for concentrations of interest is ",
-      "recommendded."
+      "than at most active individual drug. Vertical and horizontal lines can ",
+      "be added to illustrate the activity thresholds of the individual drugs ",
+      "(e.g. MIC). Activity (% killing) is not depicted; combining this with ",
+      "a line plot for concentrations of interest is recommendded."
     ),
     link_paragraph,
     p(
       style = "font-size:0.75em",
       "Anti-Biofilm Combination Index (ABCI) [Citation] for combinations of ",
       "[Drug A] and [Drug B]. Results are the average of [X] replicates. ",
-      "Positive ABCI values indicate a combination more effective than each ",
+      "Positive ABCI values indicate a combination more effective than either ",
       "individual drug, while negative values indicate a combination less ",
-      "effective than at least the most active individual drug; see materials ",
-      "and methods for ABCI calculation. Vertical and horizontal lines ",
-      "indicate the [MBIC50] of individual drugs. Tiles labelled ‘<’ indicate ",
-      "less than [50% biofilm inhibition]. Created with ABCindex [Citation]."
+      "effective than the most active individual drug; see materials and ",
+      "methods for ABCI calculation. Vertical and horizontal lines indicate ",
+      "the [MBIC50] of individual drugs. Tiles labelled '<' indicate less ",
+      "than [50% biofilm inhibition]. Created with ABCindex [Citation]."
     )
   ),
 
   tile_split = div(
     p(
       "The colour of the tiles indicates ABCI: Positive ABCI values (top) ",
-      "indicate that the combination is more effective than any individual ",
+      "indicate that the combination is more effective than either individual ",
       "drug on its own; negative values (bottom) indicate that the ",
-      "combination is less effective than at least the most active individual ",
-      "drug. They have been split into two different plots for visually ",
-      "simplified illustrations of only positive or negative interactions. ",
+      "combination is less effective than the most active individual drug. ",
+      "They have been split into two different plots for a visually ",
+      "simplified illustration of only positive or negative interactions. ",
       "Vertical and horizontal lines can be added to illustrate the activity ",
       "thresholds of the individual drugs (e.g. MIC). Activity (% killing) is ",
       "not depicted; combining this with a line plot for concentrations of ",
@@ -205,32 +206,32 @@ plot_legends <- list(
       "Anti-Biofilm Combination Index (ABCI) [Citation] for combinations of ",
       "[Drug A] and [Drug B]. Results are the average of [X] replicates. ",
       "Positive ABCI values (top) indicate a combination more effective than ",
-      "each individual drug, while negative values (bottom) indicate a ",
-      "combination less effective than at least the most active individual ",
-      "drug; see materials and methods for ABCI calculation. Vertical and ",
-      "horizontal lines indicate the [MBIC50] of individual drugs. Tiles ",
-      "labelled ‘<’ indicate less than [50% biofilm inhibition]. Created with ",
-      "ABCindex [Citation]."
+      "either individual drug, while negative values (bottom) indicate a ",
+      "combination less effective than the most active individual drug; see ",
+      "materials and methods for ABCI calculation. Vertical and horizontal ",
+      "lines indicate the [MBIC50] of individual drugs. Tiles labelled '<' ",
+      "indicate less than [50% biofilm inhibition]. Created with ABCindex ",
+      "[Citation]."
     )
   ),
 
   line = div(
     p(
       "This is a simple representation of the percentage of biomass killed ",
-      "by the drug combinations in your assay. We recommend using the ABCI ",
+      "by the drug combinations in the assay. We recommend using the ABCI ",
       "plots to identify which concentrations are the most relevant or ",
-      "representative and choosing a maximum of six for the treatment ",
+      "representative, and choosing a maximum of six for the treatment ",
       "represented as lines. A vertical line can be added to illustrate the ",
       "activity threshold (e.g. MIC) of the drug represented on the X axis."
     ),
     link_paragraph,
     p(
       style = "font-size:0.75em",
-      "Percentage of [biofilm inhibition] of different combinations of [Drug ",
-      "A] and [Drug B], relative to the average of the untreated controls. ",
-      "Results are representative of X replicates; [error bars represent ",
-      "standard deviation]. Vertical lines indicate the [MBIC50] of [Drug A]. ",
-      "Created with ABCindex [Citation]."
+      "Percentage of [biofilm inhibition] of different combinations of ",
+      "[Drug A] and [Drug B], relative to the average of the untreated ",
+      "controls. Results are representative of X replicates; [error bars ",
+      "represent standard deviation]. Vertical lines indicate the [MBIC50] of ",
+      "[Drug A]. Created with ABCindex [Citation]."
     )
   )
 )
@@ -2055,21 +2056,22 @@ panel_results <- function(id) {
         open = NA,
 
         p(
-          "ABCI is calculated for every combination of concentrations in ",
-          "each of your experiments. Positive ABCI values indicate that the ",
-          "combination is more effective than either individual drug. ",
-          "Please refer to the ",
+          "An ABCI value is calculated for every combination of ",
+          "concentrations in each of your experiments. Positive ABCI values ",
+          "indicate that the combination is more effective than either ",
+          "individual drug, while negative values correspond to combinations ",
+          "which perform worse than the best drug alone. Please refer to the ",
           actionLink(ns("help_from_results"), "Help pages"),
           "to learn more about ABCI."
         ),
 
         HTML(r"(
-            <p>Visualize your ABCI results using <b>Dot</b> or <b>Tile</b>
-            plots. The <b>Split</b> versions separate positive and
-            negative ABCI values into two plots, for visual simplicity.
-            Alternatively, the <b>Line</b> plot displays antimicrobial
-            activity for all or a subset of concentrations.</p>
-          )"),
+          <p>Visualize your ABCI results using <b>Dot</b> or <b>Tile</b>
+          plots. The <b>Split</b> versions separate positive and
+          negative ABCI values into two plots, for visual simplicity.
+          Alternatively, the <b>Line</b> plot displays antimicrobial
+          activity for all or a subset of concentrations.</p>
+        )"),
 
         disabled(
           actionButton(
@@ -3710,7 +3712,7 @@ server_results <- function(id, data) {
 
     observeEvent(input$plot_download_button, {
       showModal(modalDialog(
-        title = "Download the plot",
+        title = "Save the plot",
         size = "m",
         p(
           "Use the buttons below to download the current plot as a PNG, SVG, ",

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 # ABCindex
 
 <!-- badges: start -->
+![Deployed version](https://img.shields.io/github/r-package/v/hancockinformatics/ABCindex/main?label=Deployed)
 ![shinyapps.io](https://github.com/hancockinformatics/ABCindex/actions/workflows/shiny-deploy.yaml/badge.svg)
 <!-- badges: end -->
 

diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.1",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "RSPM",