Question

Adding text labels to PCA plot

0

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John ▴ 30

@john-9676

Last seen 5.9 years ago

dds = makeExampleDESeqDataSet(betaSD=1)
vsd = varianceStabilizingTransformation(dds)
p = plotPCA(vsd)
print(p)

## Add text labels (for presentation graphics, consider additional
## layout operations that avoid overplotting, such as the FField package on CRAN)
names = colData(vsd)$sample

p = update(p, panel = function(x, y, ...) {
      lattice::panel.xyplot(x, y, ...);
      lattice::ltext(x=x, y=y, labels=names, pos=1, offset=1, cex=0.8)
    })
print(p)

This doesn't work:

Error in update.default(p, panel = function(x, y, ...) { :

need an object with call component

How can I make this work?

Thank you for the help.

J.

deseq2 • 8.9k views

ADD COMMENT • link 8.1 years ago John ▴ 30

2

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A quick answer would be something like this:

library(ggplot2)
p <- plotPCA(vsd)
p <- p + geom_text(aes_string(x = "PC1", y = "PC2", label = "name"), color = "black")
print(p)

ADD REPLY • link 8.1 years ago Mike Smith ★ 6.5k

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Thanks Mike.

Also for others viewing the thread, if you get stuck trying to customize this plot, you can also directly use ggplot().

In the DESeq2 vignette search for the text: "It is also possible to customize the PCA plot using the ggplot function."

ADD REPLY • link 8.1 years ago Michael Love 41k

score 0 · Answer 1 · 2016-03-03

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John ▴ 30

@john-9676

Last seen 5.9 years ago

Thanks a lot Mike.

ADD COMMENT • link 8.1 years ago John ▴ 30