How to highlight DE genes in plotMD ?

Question

[Björn]

How to highlight the DE genes with FDR =0.10 using plotMD as we usually see in volcanoplot? Example figures are given below ![volcanoplot][1] [1]: https://ibb.co/fEZejx ![maplot][1] [1]: https://ibb.co/mZ3dcH How to create volcanoplot in edgeR using coefficient of contrasts.

[Nicolas Rosewick]

Could you give use a reproducible example of your input dataset please ?

[Björn]

I found solution here http://www.sthda.com/english/wiki/ggplot2-texts-add-text-annotations-to-a-graph-in-r-software

Install ggplot2

install.packages("ggplot2")

Install ggrepel

install.packages("ggrepel")

[cpad0112]

plotMD doesn't use ggplot graphing system as backend. It uses plotwithhighlights as engine and probably supports values function to highlight genes of interest.

Answer 1

[valizad2]

I don't understand how you used ggplot on plotMD. It doesn't seem to be compatible with it.

Answer 2

[raulgcova97]

Hi I managed to add DE tags to the plotMD using the code I published on Kaggle: Kaggle DE analysis

Here is an example of the code used:

fit <- glmQLFit(d, design)
qlftest<-glmQLFTest(fit, coef=i)
results <- as.data.frame(topTags(qlftest,n = Inf))
plotMD(qlftest,main="Mean-Difference Control vs T15")
text(results$logCPM,results$logFC,labels = rownames(results),col="black",cex=0.5,pos=3)

Here is the result:

Also here is the original code which I took as reference (Author: Charleen D. Adams): Differential expression (ER-/ER+) for 125 breast cancers