first try of interactive pca

SCRIPTS/DE/qualityControl.R

 #!/usr/bin/env RScript
 
 library(ggplot2)
+library(ggiraph)
 library(grid)
 library(optparse)
 
@@ -49,9 +50,10 @@ ACP<-function(d,transpose=T,scale=F,center=T) {
 
 acp2d<-function(pca, comp=1:2, group=NULL, plotVars = FALSE, pointSize=2, plotText=FALSE, fixedCoord=FALSE, main=NULL, ellipse=FALSE, color=NULL){
         if(!require("ggplot2")) stop("You must install ggplot2");
+        if(!require("ggiraph")) stop("You must install ggiraph");
         if(length(comp)!=2) stop("You must give a vector of 2 integer for comp parameter");
         percentVar <- pca$percentVar
-        functPlot<-ifelse(plotText,geom_text,geom_point)
+        functPlot<-ifelse(plotText, geom_text_interactive, geom_point_interactive)
         coor=ifelse(plotVars,"rotation","x")
         ngroup <- 0
         if(is.null(group)){
@@ -81,7 +83,7 @@ acp2d<-function(pca, comp=1:2, group=NULL, plotVars = FALSE, pointSize=2, plotTe
                     override.aes = list(size=legend_text_size/(2*pointSize)) # adjust dot size into legend
                 ))
                                                    
-        graph <- graph + functPlot(size=pointSize)+
+        graph <- graph + functPlot(size=pointSize, tooltip = rownames(d)) +
                 xlab(paste0("PC",comp[1],": ",round(percentVar[comp[1]] * 100),"% variance")) +
                 ylab(paste0("PC",comp[2],": ",round(percentVar[comp[2]] * 100),"% variance"))
         if(fixedCoord)graph <- graph + coord_fixed(ratio=percentVar[comp[2]]/percentVar[comp[1]])
@@ -165,6 +167,7 @@ compo=length(which(acpT$percentVar>0.05))+1
 exprDatT<-exprDatT[,c(rownames(sampleAnnot))]
 
 pdf(file = paste(outputDir,"/NormAndPCA.pdf",sep=""),width=10,height=10)
+acpTa <- NULL
 
 if(batchEffect || plateBatch){
         
@@ -197,9 +200,12 @@ if(batchEffect || plateBatch){
                 acp2d(acpTa,comp=c(1,2),plotText = TRUE,group = sampleAnnot[,batchEffectCol],main="PCA on normalized/transformed/adjusted data")
         }
 
+	p <- acp2d(acpTa,comp=c(1,2),group = sampleAnnot[,condCol],main="PCA on normalized/transformed/adjusted data")
+        htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 6, height_svg = 4), paste(outputDir, "PCA.html", sep="/"))
+
 	png(paste(outputDir,"/PCA.png",sep=""),width=15,height=10,units="cm",res=300,pointsize=6)
-	acp2d(acpTa,comp=c(1,2),group = sampleAnnot[,condCol],main="PCA on normalized/transformed/adjusted data")
-	dev.off()
+	print(p)
+        dev.off()
 
 	plotAllACP(compo,acpTa,sampleAnnot,condCol)
 
@@ -210,12 +216,16 @@ if(batchEffect || plateBatch){
 	barplot(acpT$percentVar*100,names.arg = round(acpT$percentVar*100,2),main = "Contribution of each component in the PCA")
 	plotAllACP(compo,acpT,sampleAnnot,condCol)
 
+	p <- acp2d(acpT,comp=c(1,2),group = sampleAnnot[,condCol],main="PCA on normalized/transformed data")
+        htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 6, height_svg = 4), paste(outputDir, "PCA.html", sep="/"))
+
         png(paste(outputDir,"/PCA.png",sep=""),width=15,height=10,units="cm",res=300,pointsize=6)
-        acp2d(acpT,comp=c(1,2),group = sampleAnnot[,condCol],main="PCA on normalized/transformed data")
+        print(p)
         dev.off()
 
 }
 
 dev.off()
 
+save(acpT, acpTa, sampleAnnot, file=paste(outputDir, "/PCA.RData", sep=""))