Hi, I have a similar problem as what was discussed here: Emperor: custom axis and numeric data error but I have the latest version of QIIME 2 (QIIME 2 release: 2018.2 QIIME 2 version: 2018.2.0 q2cli version: 2018.2.0) so the solution found doesn't help me.
When I run
qiime emperor plot
--m-metadata-file ../Aerobic-metadata-emp.tsv
--i-pcoa weighted_unifrac_pcoa_results.qza
--p-custom-axes IndivNum
--o-visualization weighted_unifrac_pcoa_indivnum.qzv
I get the error:
All values in a custom axis must be numeric, this summary shows the invalid values and the number of times they were found in column 'IndivNum':
NaN 1
I checked my metadata file in the IndivNum and they're all number values.. I even changed my ones into fours to see if that would help and it didn't. Attached is my metadata file.
I took a look at your metadata file (thanks for attaching!), and I agree, nothing looks out of place there. The particular error you are reporting looks like it has to do with missing data, though - is it possible that there is a sample present in your weighted unifrac results that isn’t in your metadata? One way to check is to run feature-table summarize on the table used to generate that file (if it was generated as part of diversity core-metrics that table is save in the --o-rarefied-table value. Take a peek at that and let us know what you find! We will get to the bottom of this!
Yes this fixed the problem! Thank you very much for your advice, and just a shutout to this forum in general, I really appreciate the support that is provided here.
