diff --git a/NAMESPACE b/NAMESPACE index 536447dc4363da21c7252ad635c0b312b90cac29..80af5eff4515f2aeb3c06a9a50bdd273102f968f 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,4 +1,5 @@ # Generated by roxygen2: do not edit by hand export(coGSEA) +export(comparResumPlot) export(generateSummaryPlots) diff --git a/R/comparResumPlot.r b/R/comparResumPlot.r index 007ce1d8488c61104429b9e9315db5066019ad1d..1868e1205f5ddbbd1b6584e42827e89e41e6e243 100644 --- a/R/comparResumPlot.r +++ b/R/comparResumPlot.r @@ -1,8 +1,18 @@ -#' 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") diff --git a/man/comparResumPlot.Rd b/man/comparResumPlot.Rd new file mode 100644 index 0000000000000000000000000000000000000000..14089bc482b289a292dde48a83d8f9b912ab859a --- /dev/null +++ b/man/comparResumPlot.Rd @@ -0,0 +1,29 @@ +% 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/")) +} +} diff --git a/man/generateSummaryPlots.Rd b/man/generateSummaryPlots.Rd index 5cbc1b7f82e741dc4e9b1aa88b4226ceb2b23be3..3e424085bce12420458863eb8f704c63071b9edb 100644 --- a/man/generateSummaryPlots.Rd +++ b/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