I'm trying to use qiime2r to make stacked taxomonic barplots. I followed the tutorial with moving-pictures files everything works great. However, when I use my data I have issues. When I manually add a #q2:types row to my metadata, the read_q2metadata() command throws an error:
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
scan() expected 'a real', got 'Blank'
I can successfully read in my metadata using:
read.table("metadata-trial2.tsv", sep="\t", comment.char="", header=T)
When I take a look at this dataframe in R all looks right with the world (although I notice that "sample-id" stays "sample-id" whereas in the moving-pictures metadata file, "sample-id" is converted to "SampleID" after read_q2metadata() which seems to suggest that R is viewing my metadata file differently).
My issue manifests when I plot using taxa_barplot(taxasums, metadata, "Treatment"). The resulting barplot does not have facets by Treatment. Instead, all bars are together with a glaring NA at the top. I suspect 3 potential causes of this problem but I'm not sure how to figure out which and solve the problem.
- my metadata.tsv is not formatted correctly.
- my metadata.tsv is not being read into R correctly.
- my metadata files does have more rows/samples than are in my table.qza artifact because of filtering steps in qiime. I'm not sure if this is causing an issue, and whether my metadata has to be a direct match with the samples in my table.qza.
Thanks for your help! I really appreciate the qiime2R package.