Emperor biplot issues and suggestions on biplot plotting software

[Zhu Wenhan]

Dear Qiime Community, 

I am trying to find out the taxa that are driving the difference in PCoA using emperor. I ran the following codes: 

summarize_taxa.py -i IL10.biom -o ./tax

make_emperor.py -i unweighted_unifrac_pc.txt -t /Volumes/LUCKY_BELLY/IL10_core_div_20000/tax/IL10_L3.txt -m /Volumes/LUCKY_BELLY/IL10_core_div_20000/IL_10_mapping_file.txt -o unweigted_L3_biplot

I got the biplot to work, but all the arrows that are present in the sample presented on http://emperor.microbio.me/master/make_emperor/biplot/index.html are missing in my plot. 

Any advice will be appreciated! 

Also, it seems that Emperor is not the most popular way to generate biplot. Can anyone suggest software packages that can take qiime data and generate biplot easily? 

Thanks! 

Best, 

Wenhan

[Yoshiki Vázquez Baeza]

Hello Wenhan,

The version of Emperor that plots biplots with arrows is 0.9.60, if you can upgrade emperor to that version, then you'll see the arrows. To do this you would run:

pip install emperor==0.9.60

You might need admin permissions to do this.

As for other alternatives for plotting biplots, using R and vegan seems to be the most popular alternative.

Thanks!

Yoshiki.

[Zhu Wenhan]

Thank you Yoshiki! That solved the issue! 

Best, 

Wenhan