Is there any way to choose PC2, PC3, PC4 instead of PC1, PC2, PC3 to plot PCoA? PC1 is too redundant and sensitive in my case. It quite strongly separates samples of different projects (especially in weighted unifrac).
Welcome to the forum!
I assume you're looking at plots in emperor?
Go to the "axes" tab in the menu
When you click on it, you'll see several options for formatting your axes, including drop downs on all three displayed axes and you can change them there.
Oh, I totally missed any other options in emperor menu except “color”
Thank you very much!!
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