Merge pull request #83 from PF2-pasteur-fr/development

Development
PF2-pasteur-fr · Jun 8, 2021 · 7c8fe50 · 7c8fe50
2 parents 2b95eaa + ea06750
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.7.3
-Date: 2020-04-29
+Version: 1.7.4
+Date: 2021-06-08
 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),
+	edgeR (>= 3.34.0),
 	ggplot2 (>= 3.3.0),
 	kableExtra
 Imports: genefilter (>= 1.44.0),
@@ -33,4 +33,4 @@ VignetteBuilder: knitr, rmarkdown
 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: 7.1.0
+RoxygenNote: 7.1.1
diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.7.4
+------------------------
+	o fixed a bug in MDSPlot()
+	o SARTools now depends on edgeR 3.34.0
+
 CHANGES IN VERSION 1.7.3
 ------------------------
 	o added some parameters to change the ggplot theme

diff --git a/R/MAPlot.R b/R/MAPlot.R
@@ -27,14 +27,16 @@ MAPlot <- function(complete, alpha=0.05, outfile=TRUE, log2FClim=NULL, ggplot_th
     complete.name$outfield <- factor(ifelse(py > ymax, "top", ifelse(py < -ymax, "bottom", "in")), 
                                      levels=c("bottom", "in", "top"))
     p[[name]] <- ggplot(data=complete.name, 
-                        aes(x=.data$baseMean, y=.data$log2FoldChange, color=.data$DE, fill=.data$DE, shape=.data$outfield)) +
+                        aes(x=.data$baseMean, y=.data$log2FoldChange,
+                            color=.data$DE, fill=.data$DE,
+                            shape=.data$outfield)) +
       scale_x_continuous(trans = log10_trans(),
                          breaks = trans_breaks("log10", function(x) 10^x),
                          labels = trans_format("log10", math_format(~10^.x))) +
-      geom_point(show.legend=FALSE, alpha=0.5, size=0.8) +
+      geom_point(show.legend=FALSE, alpha=0.5, size=1.8, stroke=0) +
+      scale_fill_manual(values=c("no"="black", "yes"="red"), drop=FALSE) +
       scale_colour_manual(values=c("no"="black", "yes"="red"), drop=FALSE) +
       scale_shape_manual(values=c("bottom"=25, "in"=21, "top"=24), drop=FALSE) +
-      scale_fill_manual(values=c("no"="black", "yes"="red"), drop=FALSE) +
       scale_y_continuous(expand=expansion(mult=c(0.03, 0.03))) +
       xlab("Mean of normalized counts") +
       ylab(expression(log[2]~fold~change)) +

diff --git a/R/MDSPlot.R b/R/MDSPlot.R
@@ -12,12 +12,12 @@
 #' @return A file named MDS.png in the figures directory
 #' @author Marie-Agnes Dillies and Hugo Varet
 
-MDSPlot <- function(dge, group, n=min(500, nrow(dge$counts)), gene.selection=c("pairwise", "common", ggplot_theme=theme_gray()),
+MDSPlot <- function(dge, group, n=min(500, nrow(dge$counts)), gene.selection=c("pairwise", "common"),
                     col=c("lightblue","orange","MediumVioletRed","SpringGreen"), outfile=TRUE, ggplot_theme=theme_gray()){
   if (outfile) png(filename="figures/MDS.png", width=1800, height=1800, res=300)
     coord <- plotMDS(dge, top=n, method="logFC", gene.selection=gene.selection[1], plot=FALSE)
     d <- data.frame(x=coord$x, y=coord$y, group = group, 
-                    sample = factor(names(coord$x), levels = names(coord$x)))
+                    factor(colnames(coord$distance.matrix.squared), levels = colnames(coord$distance.matrix.squared)))
     print(ggplot(data=d, aes(x=.data$x, y=.data$y, color=group, label=sample)) + 
       geom_point(show.legend=TRUE, size=3) +
       labs(color="") +

diff --git a/R/dispersionsPlot.R b/R/dispersionsPlot.R
@@ -41,17 +41,19 @@ dispersionsPlot <- function(dds, outfile=TRUE, ggplot_theme=theme_gray()){
   disp <- mcols(dds)$dispGeneEst
   disp <- disp[!is.na(disp)]
   disp <- disp[disp>1e-8]
-  disp <- log(disp)
-  mean.disp <- mean(disp,na.rm=TRUE)
-  sd.disp <- sd(disp,na.rm=TRUE)
   d <- data.frame(disp)
   p2 <- ggplot(data=d, aes(x=.data$disp)) +
     geom_histogram(bins=80, aes(y=.data$..density..)) +
+    scale_x_continuous(trans = log10_trans(),
+                       breaks = trans_breaks("log10", function(x) 10^x),
+                       labels = trans_format("log10", math_format())) +
     scale_y_continuous(expand=expansion(mult=c(0.01, 0.05))) +
     xlab("Feature dispersion estimate") +
     ylab("Density") +
     ggtitle("log-normality dispersion diagnostic") +
-    stat_function(fun = dnorm, args = list(mean = mean.disp, sd = sd.disp)) +
+    stat_function(fun = function(x, ...){dnorm(log10(x), ...)}, 
+                  args = list(mean = mean(log10(disp), na.rm=TRUE), 
+                              sd = sd(log10(disp), na.rm=TRUE))) +
     ggplot_theme
 
   grid.arrange(p1, p2, layout_matrix=matrix(c(1, 1, 1, 1, 1, 2, 2, 2, 2), nrow=1))

diff --git a/man/MDSPlot.Rd b/man/MDSPlot.Rd
diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### November 28th, 2019
-### designed to be executed with SARTools 1.7.3
+### designed to be executed with SARTools 1.7.4
 ################################################################################
 
 ################################################################################

diff --git a/template_script_DESeq2_CL.r b/template_script_DESeq2_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### November 28th, 2019
-### designed to be executed with SARTools 1.7.2
+### designed to be executed with SARTools 1.7.4
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 

diff --git a/template_script_edgeR.r b/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### November 28th, 2019
-### designed to be executed with SARTools 1.7.3
+### designed to be executed with SARTools 1.7.4
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR_CL.r b/template_script_edgeR_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### November 28th, 2019
-### designed to be executed with SARTools 1.7.2
+### designed to be executed with SARTools 1.7.4
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################