I just got a follow-up question regarding to the ellipsoid opacity.
I modified the command lines so I had 100 rarefied files each sampled 500 sequences. I did all the beta_diversity, upgma, pcoa steps and got the 2D graph. Here is the command line I typed in
qiime@qiime-VirtualBox:~/Desktop/Shared_Folder/fpnor4truncatewithnewversion$ make_2d_plots.py -i beta_div_weighted_pcoa_results -m fpivy.txt -b 'Treatment,StudentName' -o beta_div_PCOA_2D --scree
So I was using the default ellipsoid opacity = 0.33 and method = iqr.
My question is, what exactly does ellipsoid opacity mean? Is it referred to the variation within the 100 rarefied files? or in other words,is it fare to say 'an ellipsoid with larger shadow has greater variation within that 100 rarefied files'? What do I need to specify a value or use the default value for that? I attached a screen shot of my 2d plot.
My second question is, is there anyway to plot the 4th pcoa?
Thanks a lot!