update in doc

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(coGSEA)
+export(comparResumPlot)
 export(generateSummaryPlots)

R/comparResumPlot.r

 
-#' Internal function for coGSEA
+#' Internal coGSEA function
 #'
+#' @param preparedData  output of prepareData
+#' @param savePlot boolen
+#' @param legend boolean
+#' @param directoryPath character
+#' @return nothing
+#' @examples
+#'\dontrun{
+#'comparResumPlot(preparedData = preparedData, directoryPath = paste0(directoryPath,"/plots/"))
+#'}
 #' @export
 
+
 comparResumPlot = function(preparedData, savePlot = TRUE, legend = TRUE, directoryPath = directoryPath){
     print("Plotting Summary comparison Plot for all conditions")
     generateSummaryPlots(comparisonSummaryData(preparedData), savePlot = savePlot, legend = legend, file.name = paste(directoryPath, "_comparison_sumplot", sep = ""), format = "pdf")

man/comparResumPlot.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/comparResumPlot.r
+\name{comparResumPlot}
+\alias{comparResumPlot}
+\title{Internal coGSEA function}
+\usage{
+comparResumPlot(preparedData, savePlot = TRUE, legend = TRUE,
+  directoryPath = directoryPath)
+}
+\arguments{
+\item{preparedData}{output of prepareData}
+
+\item{savePlot}{boolen}
+
+\item{legend}{boolean}
+
+\item{directoryPath}{character}
+}
+\value{
+nothing
+}
+\description{
+Internal coGSEA function
+}
+\examples{
+\dontrun{
+comparResumPlot(preparedData = preparedData, directoryPath = paste0(directoryPath,"/plots/"))
+}
+}

man/generateSummaryPlots.Rd

@@ -6,7 +6,7 @@
 \usage{
 generateSummaryPlots(plot.data, file.name = "resumPlot",
   Xlab = "-log10(p-value)", Ylab = "Average Absolute logFC",
-  format = NULL, firstN = 10, savePlot = TRUE)
+  format = NULL, firstN = 10, savePlot = TRUE, legend = TRUE)
 }
 \arguments{
 \item{plot.data}{A dataframe formatted for this function. Output of coGSEA$resumPlot2}
@@ -20,6 +20,8 @@ generateSummaryPlots(plot.data, file.name = "resumPlot",
 \item{savePlot}{Wheter to save the plot, or just display it (boolean)}
 
 \item{Ybal}{label for Y axis (character)}
+
+\item{legen}{whether to display or not the legend if savePlot = FALSE (boolean)}
 }
 \value{
 A plot if savePlot = TRUE, else nothing