Merge pull request #177 from Open-Systems-Pharmacology/adding_examples

adding vignette urls to docs

R/plot-boxwhisker.R

@@ -1,18 +1,25 @@
 #' @title plotBoxWhisker
-#' @param data data.frame (or list of data.frames? TO BE DISCUSSED)
+#'
+#' @param data A data.frame (or list of data.frames? TO BE DISCUSSED)
 #' containing the data to be used for the plot
-#' @param metaData list of lists (structure TO BE DISCUSSED)
+#' @param metaData A list of lists (structure TO BE DISCUSSED)
 #' containing complementary information to data (e.g. unit)
 #' @param outliers logical defining if outliers should be included in boxplot
 #' @param dataMapping `BoxWhiskerDataMapping` object
 #' mapping of x, y axes + mapping of colorGrouping, sizeGrouping, shapeGrouping
-#' @param plotConfiguration `BoxWhiskerConfiguration` object
+#' @param plotConfiguration A `BoxWhiskerConfiguration` object
 #' Plot Configuration defining title, subtitle, xlabel, ylabel watermark, and legend
 #' @param plotObject
 #' ggplot object, if null creates new plot, if not add time profile layers to ggplot
+#'
 #' @description
-#' plotBoxWhisker(data, metaData, dataMapping, plotConfiguration)
+#' Producing box-and-whisker plots
+#'
 #' @return a ggplot graphical object
+#'
+#' @references For examples, see:
+#' <https://www.open-systems-pharmacology.org/TLF-Library/articles/box-whisker-vignette.html>
+#'
 #' @export
 plotBoxWhisker <- function(data,
                            metaData = NULL,

R/plot-pkratio.R

@@ -1,23 +1,32 @@
 #' @title plotPKRatio
+#'
 #' @param data data.frame containing the data to be used for the plot
-#' @param metaData list of lists
-#' containing complementary information to data (e.g. their unit and dimension).
-#' This parameter is optional.
-#' @param dataMapping
-#' `PKRatioDataMapping` class or subclass mapping x and y variables to `data` variable names.
-#' `dataMapping` provides also the values of the PK Ratio limits plotted as horizontal lines.
-#' This parameter is optional: the `tlf` library provides a smart mapping if only `data` is provided
-#' and default values of the PK Ratio limits.
-#' @param plotConfiguration
-#' `PKRatioPlotConfiguration` class or subclass defining labels, grid, background and watermark
-#' This parameter is optional: the `tlf` library provides a default configuration according to the current theme
-#' @param plotObject `ggplot` graphical object to which the PK Ratio plot layer is added
-#' This parameter is optional: the `tlf` library will initialize an empty plot if the parameter is NULL or not provided
+#' @param metaData list of lists containing complementary information to data
+#'   (e.g. their unit and dimension). This parameter is optional.
+#' @param dataMapping A `PKRatioDataMapping` class or subclass mapping x and y
+#'   variables to `data` variable names. `dataMapping` provides also the values
+#'   of the PK Ratio limits plotted as horizontal lines. This parameter is
+#'   optional: the `tlf` library provides a smart mapping if only `data` is
+#'   provided and default values of the PK Ratio limits.
+#' @param plotConfiguration A `PKRatioPlotConfiguration` class or subclass
+#'   defining labels, grid, background and watermark This parameter is optional:
+#'   the `tlf` library provides a default configuration according to the current
+#'   theme
+#' @param plotObject `ggplot` graphical object to which the PK Ratio plot layer
+#'   is added This parameter is optional: the `tlf` library will initialize an
+#'   empty plot if the parameter is `NULL` or not provided.
+#'
 #' @description
+#'
 #' Add PK Ratio plot layers to a `ggplot` graphical object.
 #' PK Ratio limits are plotted as horizontal lines.
 #' PK Ratios are plotted as a scatter plot.
+#'
 #' @return A `ggplot` graphical object
+#'
+#' @references For examples, see:
+#' <https://www.open-systems-pharmacology.org/TLF-Library/articles/pk-ratio-vignette.html>
+#'
 #' @export
 plotPKRatio <- function(data,
                         metaData = NULL,

R/themes.R

@@ -527,7 +527,7 @@ loadThemeFromJson <- function(jsonFile) {
     }
     propertyFields <- names(themeContent[[themeProperty]])
     for (propertyField in propertyFields) {
-      if(isIncluded(themeProperty, "aestheticMaps")){
+      if (isIncluded(themeProperty, "aestheticMaps")) {
         propertyExpression <- parse(text = paste0(
           themeProperty, "$", propertyField, " <- themeContent$", themeProperty, "$", propertyField
         ))
@@ -549,7 +549,7 @@ loadThemeFromJson <- function(jsonFile) {
     background$watermark <- themeContent$background$watermark
     background$legendPosition <- themeContent$background$legendPosition
   }
-  
+
   return(Theme$new(
     fonts = fonts,
     background = background,

R/utilities-aesthetics.R

@@ -27,14 +27,14 @@ Linetypes <- enum(c(
 #' @export
 Shapes <- list(
   "circle" = "circle",
-  "square" = 'square',
+  "square" = "square",
   "diamond" = "diamond",
   "triangle" = "triangle",
   "triangleDown" = "triangle down filled",
   "cross" = "cross",
   "plus" = "plus",
   "asterisk" = "asterisk",
-  "blank" = ' ',
+  "blank" = " ",
   "dot" = "bullet",
   "hollowCircle" = "circle open",
   "hollowSquare" = "square open",
@@ -70,7 +70,7 @@ asPlotShape <- function(shapes) {
   ggplotShapes <- NULL
   for (shape in shapes) {
     ggplotShape <- as.character(shape)
-    if(isIncluded(ggplotShape, names(Shapes))){
+    if (isIncluded(ggplotShape, names(Shapes))) {
       ggplotShape <- Shapes[[shape]]
     }
     ggplotShapes <- c(ggplotShapes, ggplotShape)

vignettes/atom-plots.Rmd

@@ -54,6 +54,7 @@ The output plot from *initializePlot()* is a regular `ggplot` object to which a
 Since this method is at the core of every atom and molecule plots of the `tlf`-library, any plot generated using this package will include a *plotConfiguration* field.
 
 Below are a few examples of use case of *initializePlot*:
+
 ```{r initializePlot}
 # Inintialize an empty plot without specific configuration, use the current theme
 emptyPlot <- initializePlot()