1.4.1

PF2-pasteur-fr · May 2, 2017 · 9890059 · 9890059
1 parent b261284
commit 9890059
Show file tree

Hide file tree

Showing 44 changed files with 40 additions and 56 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.4.1
-Date: 2017-03-21
+Date: 2017-05-02
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable

diff --git a/NEWS b/NEWS
@@ -1,6 +1,7 @@
 CHANGES IN VERSION 1.4.1
 ------------------------
 	o SARTools now accepts count files generated by featureCounts (still one count file per sample)
+	o added sample names and colors to the diagnostic of the size factors with DESeq2
 
 CHANGES IN VERSION 1.4.0
 ------------------------

diff --git a/R/diagSizeFactorsPlots.R b/R/diagSizeFactorsPlots.R
@@ -3,12 +3,15 @@
 #' Plots to assess the estimations of the size factors
 #'
 #' @param dds a \code{DESeqDataSet} object
+#' @param group factor vector of the condition from which each sample belongs
+#' @param col colors for the plots
 #' @param outfile TRUE to export the figure in a png file
 #' @param plots vector of plots to generate
 #' @return Two files in the figures directory: diagSizeFactorsHist.png containing one histogram per sample and diagSizeFactorsTC.png for a plot of the size factors vs the total number of reads
 #' @author Marie-Agnes Dillies and Hugo Varet
 
-diagSizeFactorsPlots <- function(dds, outfile=TRUE, plots=c("diag","sf_libsize")){
+diagSizeFactorsPlots <- function(dds, group, col=c("lightblue","orange","MediumVioletRed","SpringGreen"), 
+                                 outfile=TRUE, plots=c("diag","sf_libsize")){
   # histograms
   if ("diag" %in% plots){
     ncol <- ifelse(ncol(counts(dds))<=4, ceiling(sqrt(ncol(counts(dds)))), 3)
@@ -27,13 +30,22 @@ diagSizeFactorsPlots <- function(dds, outfile=TRUE, plots=c("diag","sf_libsize")
     }
     if (outfile) dev.off()
   }
-
+  
   # total read counts vs size factors
   if ("sf_libsize" %in% plots){
-    if (outfile) png(filename="figures/diagSizeFactorsTC.png",width=1800,height=1800,res=300)  
-    plot(sizeFactors(dds), colSums(counts(dds)), pch=19, las=1, xlab="Size factors",
-	 ylab="Total number of reads",main="Diagnostic: size factors vs total number of reads")
-    abline(lm(colSums(counts(dds)) ~ sizeFactors(dds) + 0), lty=2, col="grey")
+    if (outfile) png(filename="figures/diagSizeFactorsTC.png", width=1800, height=1800, res=300)  
+    sf <- sizeFactors(dds)
+    libsize <- colSums(counts(dds))/1e6
+    plot(sf, libsize, pch=16, las=1,
+         col = col[as.integer(group)],
+         xlab="Size factors", ylab="Total number of reads (millions)",
+         main="Diagnostic: size factors vs total number of reads")
+    abs <- range(sf); meanAbs <- mean(abs); abs <- abs(abs[2]-abs[1])/25;
+    ord <- range(libsize); meanOrd <- mean(ord); ord <- abs(ord[2]-ord[1])/25;
+    text(sf - ifelse(sf > meanAbs, abs, -abs), 
+         libsize - ifelse(libsize > meanOrd, ord, -ord),
+         colnames(dds), col=col[as.integer(group)])
+    abline(lm(libsize ~ sf + 0), lty=2, col="grey")
     if (outfile) dev.off()
   }
 }

diff --git a/R/summarizeResults.DESeq2.r b/R/summarizeResults.DESeq2.r
@@ -21,7 +21,7 @@ summarizeResults.DESeq2 <- function(out.DESeq2, group, independentFiltering=TRUE
   results <- out.DESeq2$results
 
   # diagnostic of the size factors
-  diagSizeFactorsPlots(dds=dds)
+  diagSizeFactorsPlots(dds=dds, group=group, col=col)
 
   # boxplots before and after normalisation
   countsBoxplots(dds, group=group, col=col)

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ To install the SARTools package from GitHub, open a R session and:
 - install DESeq2, edgeR and genefilter with `source("http://bioconductor.org/biocLite.R")` and `biocLite(c("DESeq2", "edgeR", "genefilter"))` (if not installed yet)
 - install devtools with `install.packages("devtools")` (if not installed yet)
 - Note: Ubuntu users may have to install some libraries (libxml2-dev, libcurl4-openssl-dev and libssl-dev) to be able to install DESeq2 and devtools
-- for Windows users only, install [Rtools](http://cran.r-project.org/bin/windows/Rtools/) or check that it is already installed (needed to build the package)
+- for Windows users only, install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) or check that it is already installed (needed to build the package)
 - load the devtools R package with `library(devtools)`
 - run `install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)`
 

diff --git a/man/BCVPlot.Rd b/man/BCVPlot.Rd
diff --git a/man/MAPlot.Rd b/man/MAPlot.Rd
diff --git a/man/MDSPlot.Rd b/man/MDSPlot.Rd
diff --git a/man/PCAPlot.Rd b/man/PCAPlot.Rd
diff --git a/man/SARTools-package.Rd b/man/SARTools-package.Rd
diff --git a/man/SERE.Rd b/man/SERE.Rd
diff --git a/man/barplotNull.Rd b/man/barplotNull.Rd
diff --git a/man/barplotTotal.Rd b/man/barplotTotal.Rd
diff --git a/man/checkParameters.DESeq2.Rd b/man/checkParameters.DESeq2.Rd
diff --git a/man/checkParameters.edgeR.Rd b/man/checkParameters.edgeR.Rd
diff --git a/man/clusterPlot.Rd b/man/clusterPlot.Rd
diff --git a/man/countsBoxplots.Rd b/man/countsBoxplots.Rd
diff --git a/man/densityPlot.Rd b/man/densityPlot.Rd
diff --git a/man/descriptionPlots.Rd b/man/descriptionPlots.Rd
diff --git a/man/diagSizeFactorsPlots.Rd b/man/diagSizeFactorsPlots.Rd
diff --git a/man/dispersionsPlot.Rd b/man/dispersionsPlot.Rd
diff --git a/man/exploreCounts.Rd b/man/exploreCounts.Rd
diff --git a/man/exportResults.DESeq2.Rd b/man/exportResults.DESeq2.Rd
diff --git a/man/exportResults.edgeR.Rd b/man/exportResults.edgeR.Rd
diff --git a/man/loadCountData.Rd b/man/loadCountData.Rd
diff --git a/man/loadTargetFile.Rd b/man/loadTargetFile.Rd
diff --git a/man/majSequences.Rd b/man/majSequences.Rd
diff --git a/man/nDiffTotal.Rd b/man/nDiffTotal.Rd
diff --git a/man/pairwiseScatterPlots.Rd b/man/pairwiseScatterPlots.Rd
diff --git a/man/rawpHist.Rd b/man/rawpHist.Rd
diff --git a/man/removeNull.Rd b/man/removeNull.Rd
diff --git a/man/run.DESeq2.Rd b/man/run.DESeq2.Rd
diff --git a/man/run.edgeR.Rd b/man/run.edgeR.Rd
diff --git a/man/summarizeResults.DESeq2.Rd b/man/summarizeResults.DESeq2.Rd
diff --git a/man/summarizeResults.edgeR.Rd b/man/summarizeResults.edgeR.Rd
diff --git a/man/tabIndepFiltering.Rd b/man/tabIndepFiltering.Rd
diff --git a/man/tabSERE.Rd b/man/tabSERE.Rd
diff --git a/man/volcanoPlot.Rd b/man/volcanoPlot.Rd
diff --git a/man/writeReport.DESeq2.Rd b/man/writeReport.DESeq2.Rd
diff --git a/man/writeReport.edgeR.Rd b/man/writeReport.edgeR.Rd
diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
-### May 9th, 2016
-### designed to be executed with SARTools 1.4.0
+### May 2nd, 2017
+### designed to be executed with SARTools 1.4.1
 ################################################################################
 
 ################################################################################

diff --git a/template_script_DESeq2_CL.r b/template_script_DESeq2_CL.r
@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
-### November 28th, 2016
-### designed to be executed with SARTools 1.4.0
+### May 2nd, 2017
+### designed to be executed with SARTools 1.4.1
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 

diff --git a/template_script_edgeR.r b/template_script_edgeR.r
@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
-### May 9th, 2016
-### designed to be executed with SARTools 1.4.0
+### May 2nd, 2017
+### designed to be executed with SARTools 1.4.1
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR_CL.r b/template_script_edgeR_CL.r
@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
-### November 28th, 2016
-### designed to be executed with SARTools 1.4.0
+### May 2nd, 2017
+### designed to be executed with SARTools 1.4.1
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################