identifying the samples on plotPCA
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@lirongrossmann-13938
Last seen 23 months ago

Hi everyone,

I am using deseq2 to find DEG between two groups. I transformed the data using the variance stabilizing transformation and plotted PCA. 

I want to label the samples on the PCA plot, is there a way to do it?

Here is my code:

dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Response)

dds <- estimateSizeFactors(dds)

vsd <- varianceStabilizingTransformation(dds)

plotPCA(vsd, intgroup="Response")

Thank you!!

deseq2 plotpca PCa • 5.1k views
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9
Entering edit mode
@mikelove
Last seen 3 days ago
United States

You can just add a geom_text():

library(DESeq2)
dds <- makeExampleDESeqDataSet(n=10000)
vsd <- vst(dds)
library(ggplot2)
plotPCA(vsd) + geom_text(aes(label=name),vjust=2)
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