Question

Biplot environmental variables on top of PCA

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ecg1g15 ▴ 30

@ecg1g15-19970

Last seen 4.1 years 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. Example Biplots Or is there a way to merge the PCA I have created adding the environmental variables on top?

deseq2 biplot plotpca • 1.3k views

ADD COMMENT • link updated 4.9 years ago by Michael Love 43k • written 4.9 years ago by ecg1g15 ▴ 30

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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.

ADD REPLY • link 4.9 years ago ecg1g15 ▴ 30

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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.

ADD REPLY • link 4.9 years ago ecg1g15 ▴ 30

score 0 · Answer 1 · 2020-01-24

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Michael Love 43k

@mikelove

Last seen 10 days 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.

ADD COMMENT • link 4.9 years ago Michael Love 43k