How to highlight DE genes in plotMD ?
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3.5 years ago
Björn ▴ 100

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.

edgeR plotMD volcanoplot mirnaseq • 2.4k views
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Could you give use a reproducible example of your input dataset please ?

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

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14 months ago
valizad2 ▴ 10

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

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6 months ago

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:

plotMD

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

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