[BioC] SmearPlot edgeR - adding gene names to genes of interest

[Christine Gläßer]

Dear all,

I have used edgeR for analyzing differential expression. I also created 
a smear plot visualizing DGE results (code see below). I'd now like to 
highlight some genes of interest (they are significantly diff. 
expressed) in this plot by labeling them; do you know if there's a way 
to do so?

Kind regards, and many thanks in advance,

Christine Gläßer


###### Code ########

counts <- as.matrix(read.table(infile, header = TRUE, sep = "\t", 
row.names = 1, as.is = TRUE))
cpms<-cpm(counts)
keep <- rowSums(cpms>1)>=4  ### at least 4 replicates
counts <- counts[keep,]

group <- factor(c(1,1,1,1,1,2,2,2,2,3,3,3,3))

d <- DGEList(counts=counts, group=group)
d <- calcNormFactors(d)

design <- model.matrix(~ 0+group)
colnames(design) <- cols

contrasts <- makeContrasts(con1 = CONTRAST1, con2 =  CONTRAST2, 
levels=design)

y <- estimateGLMCommonDisp(d,design)
y <- estimateGLMTrendedDisp(y,design)
y <- estimateGLMTagwiseDisp(y,design)
fit <- glmFit(y,design)

for (i in colnames(contrasts))
{
   print (i)

   outfilename <- paste(paste(outdir, i, sep="/"))
   outfilename <- paste(paste(outfilename, ".txt", sep=""))
   outfilesmearplot <- paste(paste(outdir, i, sep="/"))
   outfilesmearplot <- paste(paste(outfilesmearplot, "_smearplot.pdf", 
sep=""))

   lrt <- glmLRT(fit, contrast=contrasts[,i])
   tt <- topTags(lrt, n=nrow(d), adjust.method="BH")
   rn <- rownames(tt$table)
   deg <- rn[tt$table$FDR < 0.05]

   pdf(outfilesmearplot)
  ###### SMEAR PLOT STARTS HERE #######
   plotSmear(d, de.tags=deg)
   abline(h = c(-1, 1), col = "dodgerblue")
   dev.off()
   write.table(tt$table, file=outfilename, sep="\t")
}