qiime2R plugin metadata

(Todd Testerman) #1


First off, I want to say that the qiime2R plugin has been great. Being able to tie in a Qiime analysis with Phyloseq graphics is really convenient.

I have been having a minor problem with import using the qza_to_phyloseq function. I am finding that my metadata file is losing the entire first column with “SampleID” as the header. I am querying the resulting phyloseq object to check:

colnames([email protected]_data)

I am not sure why this is happening. I attached a portion of the map file below:

Q2_example.txt (190 Bytes)

This is the result of colnames([email protected]_data):

“Sample_Name” “Project_Name” “Subproject” “Type”

I expect “SampleID” to be the first column, however. Would anyone be able to advise on this issue?

(Todd Testerman) #2

I think this can be closed. I realized that the header for the SampleID column is not normally retained after import into phyloseq. I was trying to figure out why a downstream phyloseq heatmap function wasn’t working and was hoping it was something that occurred during import but I don’t think that’s the problem.