Merge pull request #41 from PF2-pasteur-fr/development

Development

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.6.0
-Date: 2017-12-11
+Version: 1.6.1
+Date: 2018-03-20
 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
@@ -12,3 +12,4 @@ VignetteBuilder: knitr
 Encoding: latin1
 Description: Provide R tools and an environment for the statistical analysis of RNA-Seq projects: load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report.
 License: GPL-2
+RoxygenNote: 6.0.1

NEWS

@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.6.1
+------------------------
+	o new boolean parameter forceCairoGraph
+	o adapt size of PNG plots if width/height are too large
+
 CHANGES IN VERSION 1.6.0
 ------------------------
 	o use "percentage" instead of "proportion" in some plots

R/MAPlot.R

@@ -11,7 +11,7 @@
 MAPlot <- function(complete, alpha=0.05, outfile=TRUE){
   ncol <- ifelse(length(complete)<=4, ceiling(sqrt(length(complete))), 3)
   nrow <- ceiling(length(complete)/ncol)
-  if (outfile) png(filename="figures/MAPlot.png", width=1800*ncol, height=1800*nrow, res=300)
+  if (outfile) png(filename="figures/MAPlot.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
     par(mfrow=c(nrow,ncol))
       for (name in names(complete)){
         complete.name <- complete[[name]]

R/PCAPlot.R

@@ -20,7 +20,7 @@ PCAPlot <- function(counts.trans, group, n=min(500,nrow(counts.trans)),
   prp <- round(prp[1:3],2)
 
   # create figure
-  if (outfile) png(filename="figures/PCA.png",width=1800*2,height=1800,res=300)
+  if (outfile) png(filename="figures/PCA.png",width=cairoSizeWrapper(1800*2),height=cairoSizeWrapper(1800),res=300)
     par(mfrow=c(1,2))
 	# axes 1 et 2
 	abs=range(pca$x[,1]); abs=abs(abs[2]-abs[1])/25;

R/cairoSizeWrapper.R

@@ -0,0 +1,16 @@
+#' Cairo Size Wrapper
+#'
+#' Limits the pixel size to either to the minimum of the given and the max allowed pixel size 32767x32767 pixels if
+#' Cairo graphical has been choosen
+#'
+#' @param pixel_re requested pixel size
+#' @return the minimum between the requested and maximal allowed pixel size if Cairo is selected otherwise the requested pixel size
+#' @author vipul patel
+
+cairoSizeWrapper <- function(pixel_re){
+  if (options("bitmapType") == "cairo"){
+    return(min(pixel_re,32767))
+  } else{
+    return(pixel_re)
+  }
+}

R/diagSizeFactorsPlots.R

@@ -16,7 +16,7 @@ diagSizeFactorsPlots <- function(dds, group, col=c("lightblue","orange","MediumV
   if ("diag" %in% plots){
     ncol <- ifelse(ncol(counts(dds))<=4, ceiling(sqrt(ncol(counts(dds)))), 3)
     nrow <- ceiling(ncol(counts(dds))/ncol)
-    if (outfile) png(filename="figures/diagSizeFactorsHist.png", width=1400*ncol, height=1400*nrow, res=300)
+    if (outfile) png(filename="figures/diagSizeFactorsHist.png", width=cairoSizeWrapper(1400*ncol), height=cairoSizeWrapper(1400*nrow), res=300)
     par(mfrow=c(nrow,ncol))
     geomeans <- exp(rowMeans(log(counts(dds))))
     samples <- colnames(counts(dds))

R/pairwiseScatterPlots.R

@@ -11,7 +11,7 @@
 pairwiseScatterPlots <- function(counts, group, outfile=TRUE){
   ncol <- ncol(counts)
   if (ncol <= 30){
-    if (outfile) png(filename="figures/pairwiseScatter.png", width=700*ncol, height=700*ncol, res=300)
+    if (outfile) png(filename="figures/pairwiseScatter.png", width=cairoSizeWrapper(700*ncol), height=cairoSizeWrapper(700*ncol), res=300)
     # defining panel and lower.panel functions
     panel <- function(x,y,...){points(x, y, pch=".");abline(a=0,b=1,lty=2);}
     lower.panel <- function(x,y,...){

R/rawpHist.R

@@ -10,7 +10,7 @@
 rawpHist <- function(complete, outfile=TRUE){
   ncol <- ifelse(length(complete)<=4, ceiling(sqrt(length(complete))), 3)
   nrow <- ceiling(length(complete)/ncol)
-  if (outfile) png(filename="figures/rawpHist.png", width=1800*ncol, height=1800*nrow, res=300)
+  if (outfile) png(filename="figures/rawpHist.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
     par(mfrow=c(nrow,ncol))
     for (name in names(complete)){
       hist(complete[[name]][,"pvalue"], nclass=50, xlab="Raw p-value", 

R/volcanoPlot.r

@@ -11,7 +11,7 @@
 volcanoPlot <- function(complete, alpha=0.05, outfile=TRUE){
   ncol <- ifelse(length(complete)<=4, ceiling(sqrt(length(complete))), 3)
   nrow <- ceiling(length(complete)/ncol)
-  if (outfile) png(filename="figures/volcanoPlot.png", width=1800*ncol, height=1800*nrow, res=300)
+  if (outfile) png(filename="figures/volcanoPlot.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
     par(mfrow=c(nrow,ncol))
     for (name in names(complete)){
       complete.name <- complete[[name]]

template_script_DESeq2.r

@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
-### Dec 11th, 2017
-### designed to be executed with SARTools 1.6.0
+### March 20th, 2018
+### designed to be executed with SARTools 1.6.1
 ################################################################################
 
 ################################################################################
@@ -37,11 +37,14 @@ locfunc <- "median"                                  # "median" (default) or "sh
 colors <- c("dodgerblue","firebrick1",               # vector of colors of each biological condition on the plots
             "MediumVioletRed","SpringGreen")
 
+forceCairoGraph <- FALSE
+
 ################################################################################
 ###                             running script                               ###
 ################################################################################
 setwd(workDir)
 library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
 
 # checking parameters
 checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,

template_script_DESeq2_CL.r

@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
-### Dec 11th, 2017
-### designed to be executed with SARTools 1.6.0
+### March 20th, 2018
+### designed to be executed with SARTools 1.6.1
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 
@@ -89,7 +89,14 @@ make_option(c("-l", "--locfunc"),
 make_option(c("-C", "--colors"),
 			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
 			dest="cols",
-			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
+			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
+
+make_option(c("-g", "--forceCairoGraph"),
+            action="store_true",
+            default=FALSE,
+            dest="forceCairoGraph",
+            help="activate cairo type")
+
 )
 
 # now parse the command line to check which option is given and get associated values
@@ -117,7 +124,7 @@ pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method
 typeTrans <- opt$typeTrans                           # transformation for PCA/clustering: "VST" ou "rlog"
 locfunc <- opt$locfunc                               # "median" (default) or "shorth" to estimate the size factors
 colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
-	
+forceCairoGraph <- opt$forceCairoGraph				 # force cairo as plotting device if enabled
 # print(paste("workDir", workDir))
 # print(paste("projectName", projectName))
 # print(paste("author", author))
@@ -141,6 +148,7 @@ colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each
 ################################################################################
 # setwd(workDir)
 library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
 
 # checking parameters
 problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,

template_script_edgeR.r

@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
-### Dec 11th, 2017
-### designed to be executed with SARTools 1.6.0
+### March 20th, 2018
+### designed to be executed with SARTools 1.6.1
 ################################################################################
 
 ################################################################################
@@ -35,11 +35,14 @@ normalizationMethod <- "TMM"                         # normalization method: "TM
 colors <- c("dodgerblue","firebrick1",               # vector of colors of each biological condition on the plots
             "MediumVioletRed","SpringGreen")
 
+forceCairoGraph <- FALSE
+
 ################################################################################
 ###                             running script                               ###
 ################################################################################
 setwd(workDir)
 library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
 
 # checking parameters
 checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,

template_script_edgeR_CL.r

@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
-### Dec 11th, 2017
-### designed to be executed with SARTools 1.6.0
+### March 20th, 2018
+### designed to be executed with SARTools 1.6.1
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################
 
@@ -79,7 +79,13 @@ make_option(c("-n", "--normalizationMethod"),
 make_option(c("-C", "--colors"),
 			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
 			dest="cols",
-			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
+			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
+
+make_option(c("-g", "--forceCairoGraph"),
+            action="store_true",
+            default=FALSE,
+            dest="forceCairoGraph",
+            help="activate cairo type")
 )
 
 # now parse the command line to check which option is given and get associated values
@@ -105,7 +111,7 @@ gene.selection <- opt$gene.selection                 # selection of the features
 normalizationMethod <- opt$normalizationMethod       # normalization method in calcNormFactors
 cpmCutoff <- opt$cpmCutoff                           # counts-per-million cut-off to filter low counts
 colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
-
+forceCairoGraph <- opt$forceCairoGraph				 # force cairo as plotting device if enabled
 # print(paste("workDir", workDir))
 # print(paste("projectName", projectName))
 # print(paste("author", author))
@@ -127,6 +133,7 @@ colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each
 ################################################################################
 # setwd(workDir)
 library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
 
 # checking parameters
 problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,

vignettes/SARTools.rmd

@@ -82,8 +82,8 @@ All the parameters that can be modified by the user are at the beginning of the
  - `cpmCutoff`: (if use of edgeR) counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
  - `gene.selection`: (if use of edgeR) method of selection of the features for the MultiDimensional Scaling plot (`"pairwise"` by default or `common`);
  - `normalizationMethod`: (if use of edgeR) normalization method in `calcNormFactors()`: `"TMM"` (default), `"RLE"` (DESeq method) or `"upperquartile"`;
- - `colors`: colors used for the figures (one per biological condition), 4 are given by default.
-
+ - `colors`: colors used for the figures (one per biological condition), 4 are given by default;
+ - `forceCairoGraph`: `TRUE` to force the use of cairo with `options(bitmapType="cairo")` (`FALSE` by default).
 
 All these parameters will be saved and written at the end of the HTML report in order to keep track of what has been done.