Emperor and 3D biplot PCoA

[avon...@asu.edu]

Hello!

I have used successfully the generate 3D biplots script to obtain my PCoA graphics with emperor.  But, I'm wondering if the plot obtained by using this script might have tick marks for the pcoa vectors (pc1, pc2, and pc3). Or alternatively, is there any script to obtain a 2D PCoA with taxonomy data?

I will highly appreciate your help

[Yoshiki Vázquez Baeza]

Hello,

There should be PCx labels on the plot, there's a known problem about not being able to export text as SVG, but the text should be show on screen as you are viewing the plot.

We currently don't support 2D biplots, though this is on the way along with a fair amount of improvements (see here).

An alternative you could use, would be to plot this same data in, R, Python, MATLAB, Mathematica or any other plotting platform. The files containing the principal coordinates analysis data is just a text file, a description of this file can be found here. And finally you would need the taxonomy data, which you can generate using the --biplot_fp flag of make_emperor.py, this will generate a coordinate for each of the taxa presented on screen.

Thanks!

Yoshiki.