group_pairwisescatterplot

DESCRIPTION

@@ -2,7 +2,7 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.7.2
-Date: 2019-11-28
+Date: 2020-01-13
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0),

R/descriptionPlots.r

@@ -27,7 +27,7 @@ descriptionPlots <- function(counts, group, col=c("lightblue","orange","MediumVi
   # SERE and pairwise scatter plots
   cat("Matrix of SERE statistics:\n")
   print(tabSERE(counts))
-  pairwiseScatterPlots(counts=counts, group=group)
+  pairwiseScatterPlots(counts=counts)
 
   return(majSequences)
 }

R/pairwiseScatterPlots.R

@@ -3,12 +3,11 @@
 #' Scatter plots for pairwise comparaisons of log counts
 #'
 #' @param counts \code{matrix} of raw counts
-#' @param group factor vector of the condition from which each sample belongs
 #' @param outfile TRUE to export the figure in a png file
 #' @return A file named pairwiseScatter.png in the figures directory containing a pairwise scatter plot with the SERE statistics in the lower panel
 #' @author Marie-Agnes Dillies and Hugo Varet
 
-pairwiseScatterPlots <- function(counts, group, outfile=TRUE){
+pairwiseScatterPlots <- function(counts, outfile=TRUE){
   ncol <- ncol(counts)
   if (ncol <= 12){
     if (outfile) png(filename="figures/pairwiseScatter.png", width=cairoSizeWrapper(850*ncol), height=cairoSizeWrapper(700*ncol), res=300)