Hi @Nicholas_Bokulich! So I realized pretty quickly that I was being silly and using an option that does not exist in my data set! However, I am now having the problem that I can not generate an emperor plot as none of my custom axises have solely numbers in them. I’m not sure how I work around this problem as the data that I have must contain non-numerical descriptors. here is an example of the command that I am using: qiime emperor plot --i-pcoa core-metrics-results/unweighted_unifrac_pcoa_results.qza --m-metadata-file infant-metadata3.tsv --p-custom-axis Description --o-visualization core-metrics-results/unweighted-unifrac-emperor.qzv
--p-custom-axis only accepts numerical data because it is intended, e.g., to plot the relationship between a numerical value (e.g., time) and PCoA ordination.
It sounds like what you are trying to do is separate sample groups along axis-1 using the “Description” column, which contains non-numeric data; this can still be done. What I recommend doing is creating a new metadata column that assigns “Description” values to “dummy variables”, e.g., numbers 1-n (where n = the number of unique values you have in “Description”).
Does that solve your problem? If not, please post back (and possibly provide a metadata file; you can send directly to me if you don’t want to share publicly) and we can help work through this.
Just a quick followup: @lmarple,
--p-custom-axis is optional, so if you don’t want to include an explicit numeric axis you can just omit that option.
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