shrinkage+ggplot2

Author: hvaret

DESCRIPTION

@@ -2,7 +2,7 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.8.2
-Date: 2025-03-24
+Date: 2025-10-09
 Authors@R: c(
     person(given = "Hugo", family = "Varet", role = c("aut", "cre"), email = "hugo.varet@pasteur.fr"),
     person(given = "Marie-Agnès", family = "Dillies", role = c("aut"), email = "marie-agnes.dillies@pasteur.fr")

NEWS

@@ -1,6 +1,8 @@
 CHANGES IN VERSION 1.8.2
 ------------------------
 	o use of after_stat(density) instead of ..density..
+	o fixed other few deprecated usages of ggplot2
+	o back to default DESeq2 shrinkage as "ashr" tends to produce aberrant log2FoldChanges
 
 CHANGES IN VERSION 1.8.1
 ------------------------

R/barplotNull.R

@@ -25,6 +25,6 @@ barplotNull <- function(counts, group, col=c("lightblue","orange","MediumVioletR
             ggplot_theme +
             theme(axis.text.x=element_text(angle=90, hjust=1, vjust=0.5)) +
             scale_y_continuous(expand=expansion(mult=c(0.01, 0.05))) +
-            geom_hline(yintercept=percentage.allNull, linetype="dashed", color="black", size=1))
+            geom_hline(yintercept=percentage.allNull, linetype="dashed", color="black", linewidth=1))
   if (outfile) dev.off()
 }

R/diagSizeFactorsPlots.R

@@ -31,7 +31,7 @@ diagSizeFactorsPlots <- function(dds, group, col=c("lightblue","orange","MediumV
         xlab(expression(log[2]~(counts/geometric~mean))) +
         ylab("") +
         ggtitle(paste0("Size factor diagnostic - ", samples[j])) +
-        geom_vline(xintercept=log2(sizeFactors(dds)[j]), linetype="dashed", color="red", size=1) +
+        geom_vline(xintercept=log2(sizeFactors(dds)[j]), linetype="dashed", color="red", linewidth=1) +
         ggplot_theme
     }
     tmpfun <- function(...) grid.arrange(..., nrow=nrow, ncol=ncol)

R/pairwiseScatterPlots.R

@@ -20,7 +20,7 @@ pairwiseScatterPlots <- function(counts, outfile=TRUE, ggplot_theme=theme_gray()
       for (j in 1:ncol){
         if (i==j) next
         if (i > j){
-          p[[k]] <- ggplot(data=cbind(d, z=1), aes_string(x=names(d)[i], y=names(d)[j], z="z")) +
+          p[[k]] <- ggplot(data=cbind(d, z=1), aes(x=.data[[names(d)[i]]], y=.data[[names(d)[j]]], z=.data[["z"]])) +
             stat_summary_2d(fun=function(z) log(sum(z)), bins=60, show.legend=FALSE) +
             scale_x_continuous(trans = log10_trans(),
                                breaks = trans_breaks("log10", function(x) 10^x),

R/run.DESeq2.r

@@ -34,7 +34,7 @@ run.DESeq2 <- function(counts, target, varInt, batch=NULL,
   dds <- estimateDispersions(dds, fitType=fitType)
 
   # statistical testing: perform all the comparisons between the levels of varInt
-  dds <- nbinomWaldTest(dds, ...)
+  dds <- nbinomWaldTest(dds, betaPrior=TRUE, ...)
   results <- list()
   for (comp in combn(nlevels(colData(dds)[,varInt]), 2, simplify=FALSE)){
     levelRef <- levels(colData(dds)[,varInt])[comp[1]]
@@ -43,10 +43,6 @@ run.DESeq2 <- function(counts, target, varInt, batch=NULL,
                    contrast=c(varInt, levelTest, levelRef),
                    pAdjustMethod=pAdjustMethod, cooksCutoff=cooksCutoff,
                    independentFiltering=independentFiltering, alpha=alpha)
-    lfcs <- lfcShrink(dds, res=res,
-                      contrast=c(varInt, levelTest, levelRef),
-                      type="ashr", quiet=TRUE)
-    res$log2FoldChange <- lfcs$log2FoldChange
     results[[paste0(levelTest,"_vs_",levelRef)]] <- res
     cat(paste("Comparison", levelTest, "vs", levelRef, "done\n"))
   }

inst/report_DESeq2.rmd

@@ -226,8 +226,6 @@ Figure 14 shows the volcano plots for the comparisons performed and differential
 
 </center>
 
-Note that the log2(Fold-Changes) are shrunk using the "ashr" method that has been shown to be more robust than the original "normal" method [@ashr].
-
 Full results as well as lists of differentially expressed features are provided in the following text files which can be easily read in a spreadsheet. For each comparison:
 
 - TestVsRef.complete.txt contains results for all the features;