Biplot environmental variables on top of PCA
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ecg1g15 • 0
@ecg1g15-19970
Last seen 9 months ago

Hi,

I have used the function

plotPCA(vsd, intgroup = c("location", "station"))


to visualize a PCA with all my samples (genes expressed differently on different samples, under different environmental conditions).

I would like to plot the environmental variables (conditions of the samples) with arrow on top to see the effect of the environmental variables. similar to what they do in "facto extra" -> fvizpcabiplot. Or is there a way to merge the PCA I have created adding the environmental variables on top?

deseq2 biplot plotpca • 197 views
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I have also read about the Redundancy Analysis used to correlate species matrix against environmental descriptors, is this something that would be recommended doing? I am confused as the initial df has samples in rows and genes in columns, and another df with the environmental variables.

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Entering edit mode

I have also read about the Redundancy Analysis used to correlate species matrix against environmental descriptors, is this something that would be recommended doing? I am confused as the initial df has samples in rows and genes in columns, and another df with the environmental variables.

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@mikelove
Last seen 18 hours ago
United States

See the help page for plotPCA: the easiest approach will be to compute the PCA yourself as directed in the man page.