ggplot2_density

Author: hvaret

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.8.1
-Date: 2022-03-23
+Version: 1.8.2
+Date: 2023-06-13
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <hugo.varet@pasteur.fr>
 Depends: R (>= 3.3.0),
@@ -34,4 +34,4 @@ 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: 7.1.2
+RoxygenNote: 7.2.3

NEWS

@@ -1,3 +1,7 @@
+CHANGES IN VERSION 1.8.2
+------------------------
+	o use of after_stat(density) instead of ..density..
+
 CHANGES IN VERSION 1.8.1
 ------------------------
 	o log2FoldChanges from DESeq2 are now computed using lfcShrink() with type="ashr" as "apeglm"

R/countsBoxplots.R

@@ -11,7 +11,7 @@
 #' @author Marie-Agnes Dillies and Hugo Varet
 
 countsBoxplots <- function(object, group, col = c("lightblue","orange","MediumVioletRed","SpringGreen"), outfile=TRUE, ggplot_theme=theme_gray()){
-  if (class(object)=="DESeqDataSet"){
+  if (inherits(object, "DESeqDataSet")){
     counts <- counts(object)
     counts <- removeNull(counts)
     norm.counts <- counts(object, normalized=TRUE)

R/dispersionsPlot.R

@@ -43,7 +43,7 @@ dispersionsPlot <- function(dds, outfile=TRUE, ggplot_theme=theme_gray()){
   disp <- disp[disp>1e-8]
   d <- data.frame(disp)
   p2 <- ggplot(data=d, aes(x=.data$disp)) +
-    geom_histogram(bins=80, aes(y=.data$..density..)) +
+    geom_histogram(bins=80, aes(y=after_stat(density))) +
     scale_x_continuous(trans = log10_trans(),
                        breaks = trans_breaks("log10", function(x) 10^x),
                        labels = trans_format("log10", math_format())) +

R/exploreCounts.R

@@ -14,12 +14,12 @@
 exploreCounts <- function(object, group, typeTrans="VST", gene.selection="pairwise",
                           col=c("lightblue","orange","MediumVioletRed","SpringGreen"),
                           ggplot_theme=theme_light()){
-  if (class(object)=="DESeqDataSet"){
+  if (inherits(object, "DESeqDataSet")){
     if (typeTrans == "VST") counts.trans <- assay(varianceStabilizingTransformation(object))
     else counts.trans <- assay(rlogTransformation(object))
     PCAPlot(counts.trans=counts.trans, group=group, col=col, ggplot_theme=ggplot_theme)
     clusterPlot(counts.trans=counts.trans, group=group, ggplot_theme=ggplot_theme)  
-  } else if (class(object)=="DGEList"){
+  } else if (inherits(object, "DGEList")){
     MDSPlot(dge=object, group=group, col=col, gene.selection=gene.selection, ggplot_theme=ggplot_theme)
     clusterPlot(counts.trans=cpm(object, prior.count=2, log=TRUE), group=group, ggplot_theme=ggplot_theme)  
   } else{

man/loadCountData.Rd

@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 23rd, 2022
-### designed to be executed with SARTools 1.8.1
+### designed to be executed with SARTools 1.8.2
 ################################################################################
 
 ################################################################################

template_script_DESeq2.r

@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 23rd, 2022
-### designed to be executed with SARTools 1.8.1
+### designed to be executed with SARTools 1.8.2
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 

template_script_DESeq2_CL.r

@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### March 23rd, 2022
-### designed to be executed with SARTools 1.8.1
+### designed to be executed with SARTools 1.8.2
 ################################################################################
 
 ################################################################################

template_script_edgeR.r

@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### March 23rd, 2022
-### designed to be executed with SARTools 1.8.1
+### designed to be executed with SARTools 1.8.2
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################