Adding separate color a list of genes in plotMA
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11 weeks ago
jaqx008 ▴ 90

Hello all and happy NEW YEAR. I am trying to create either plotMA, DESeq2 or VolcanoPlot such that in addition to the original plot (Usually in black and red) I can supply a list of genes (present in the plot) from the DESeq2 result to appear as separate colors (e.g green) in the plot. I haven't seen a good answer to address this, help. See my original DESeq2 command bellow.

library(DESeq2)
coldata <- read.csv("Conditions2.txt", sep = '\t')
cts <- as.matrix(read.csv("counts", sep = '\t', row.names = 1, header = TRUE))
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ Condition)
dds <- DESeq(dds)
res <- results(dds) 
write.table(res, file = "NEGvsZC.txt", sep = '\t')
pdf("NEGvsZC.pdf")
dev.off()
deseq2 plotMA VolcanoPlot R RNA-Seq • 129 views
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Entering edit mode

If external libraries are an option, I'd recommend trying Kevin Blighe's EnhancedVolcano package. That makes highly customizable volcano plots.

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Thanks for your recommendation. I am not sure what you mean by external libraries.

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I was referring to anything that's not a part of basic/default R packages (graphics, stats, etc are basic default R packages, ggplot2, ComplexHeatmap, EnhancedVolcano, dplyr etc are external libraries)

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