v 0.1.1 bars as default, docs improved

Author: quantixed

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SuperPlotR
 Title: Making SuperPlots in R
-Version: 0.1.0
+Version: 0.1.1
 Authors@R:
     person(given = "Stephen J",
            family = "Royle",

NAMESPACE

@@ -2,8 +2,11 @@
 
 export(add_sp_bars)
 export(flatplot)
+export(get_fp_color)
+export(get_fp_colors)
 export(get_fp_colour)
 export(get_fp_colours)
+export(get_sp_colors)
 export(get_sp_colours)
 export(get_sp_shapes)
 export(get_sp_stats)

NEWS.md

@@ -1,5 +1,10 @@
 # SuperPlotR
 
+## SuperPlotR 0.1.1
+
+* Use of mean ± sd bars is now the default
+* Minor changes to colour handling and documentation
+
 ## SuperPlotR 0.1.0
 
 * Test structure added. Bumping to 0.1.0 to reflect this change.

R/flatplot.R

@@ -1,11 +1,18 @@
 #' Make a FlatPlot
 #'
+#' @description
+#' The function \code{flatplot} creates a FlatPlot using \code{ggplot2}.
+#' A FlatPlot is a simplified version of a SuperPlot that does not require
+#' replicate information
+#'
 #' @param df data frame with at least three columns: meas, cond, repl
 #' @param meas character name of column with measurement (e.g. intensity)
 #' @param cond character name of column with condition (e.g. Control, WT)
+#' @param repl not required for FlatPlot, but included for consistency with SuperPlot; can be set to NULL
 #' @param colour string for colour palette to use, select ("rl_green", "rl_red",
 #' "rl_blue", "rl_purple", "rl_orange", "rl_magenta", or a hex colour, default
 #' is black)
+#' @param color valid alternative spelling of colour
 #' @param xlab string for x label (default is empty)
 #' @param ylab string for y label (default is "Measurement")
 #' @param datadist string for data distribution to use, select ("sina" default,
@@ -34,19 +41,26 @@
 #' flatplot(lord_jcb, "Speed", "Treatment", ylab = "Speed (um/min)")
 #'
 flatplot <- function(df,
-                      meas, cond,
-                      colour = "#000000",
-                      xlab = "", ylab = "Measurement",
-                      datadist = "sina",
-                      size = 2,
-                      alpha = 0.5,
-                      bars = "mean_sd",
-                      fsize = 12,
-                      gg = NULL,
-                      stats = FALSE,
-                      stats_test = "para_unpaired") {
+                     meas, cond, repl = NULL,
+                     colour = "#000000",
+                     color = NULL,  # for American users who might use color instead of colour
+                     xlab = "", ylab = "Measurement",
+                     datadist = "sina",
+                     size = 2,
+                     alpha = 0.5,
+                     bars = "mean_sd",
+                     fsize = 12,
+                     gg = NULL,
+                     stats = FALSE,
+                     stats_test = "para_unpaired") {
   ncond <- nrepl <- NULL
   rep_mean <- rep_median <- NULL
+  if (!is.null(color)) {
+    colour <- color
+  }
+  if (!is.null(repl)) {
+    warning("repl argument is not used in flatplot and will be ignored")
+  }
 
   # validate args
   validate_args(colour = colour, xlab = xlab, ylab = ylab, datadist = datadist,

R/superplot.R

@@ -1,33 +1,37 @@
 #' Make a SuperPlot
 #'
+#' @description
+#' The function \code{superplot} creates a SuperPlot using \code{ggplot2}.
+#'
 #' @param df data frame with at least three columns: meas, cond, repl
 #' @param meas character name of column with measurement (e.g. intensity)
 #' @param cond character name of column with condition (e.g. Control, WT)
 #' @param repl character name of column with replicate (e.g. unique experiment
-#' identifiers)
+#'   identifiers)
 #' @param pal name of colour palette to use (default is "tol_bright")
 #' @param xlab string for x label (default is empty)
 #' @param ylab string for y label (default is "Measurement")
 #' @param datadist string for data distribution to use, select ("sina" default,
-#' "jitter", or "violin")
+#'   "jitter", or "violin")
 #' @param size numeric vector of size range data and summary points (default is
-#' c(2, 3))
+#'   c(2, 3))
 #' @param alpha numeric vector of alpha range data and summary points (default
-#' is c(0.5, 0.7))
-#' @param bars string for type of error bars to add, select ("none" default,
-#' "mean_sd", "mean_sem", or "mean_ci")
+#'   is c(0.5, 0.7))
+#' @param bars string for type of error bars to add, select "mean_sd" (default),
+#'   "mean_sem", or "mean_ci"; for no bars use an empty string (""); for no
+#'   error bars but still show the mean with a crossbar, use "none".
 #' @param linking logical for whether to link summary points between conditions
-#' (default is FALSE)
+#'   (default is FALSE)
 #' @param fsize numeric font size for text (default is 12)
 #' @param shapes logical for whether to use different shapes for replicates
 #' @param rep_summary string for summary statistic to use for replicates, select
-#' ("rep_mean" default, or "rep_median")
+#'   ("rep_mean" default, or "rep_median")
 #' @param gg ggplot object to add to (default is NULL)
 #' @param stats logical for whether to add statistical tests (default is FALSE)
 #' @param stats_test string for statistical test to use, select
-#' ("para_unpaired", "para_paired", "nonpara_unpaired", or "nonpara_paired")
+#'   ("para_unpaired", "para_paired", "nonpara_unpaired", or "nonpara_paired")
 #' @param info logical for whether to print information about the plot (default
-#' is FALSE)
+#'   is FALSE)
 #'
 #' @return ggplot object
 #' @import ggplot2
@@ -50,7 +54,7 @@ superplot <- function(df,
                       datadist = "sina",
                       size = c(2, 3),
                       alpha = c(0.5, 0.7),
-                      bars = "",
+                      bars = "mean_sd",
                       linking = FALSE,
                       rep_summary = "rep_mean",
                       shapes = FALSE,

README.Rmd

@@ -59,7 +59,7 @@ These columns are:
 2. the experimental condition,
 3. the experimental repeat that the measurment comes from.
 
-The `superplot` function takes the data frame, the names of these three columns,
+The `superplot()` function takes the data frame, the names of these three columns,
 and is further customisable with additional arguments.
 
 See `vignette("SuperPlotR")` for more examples, or