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sterrettJD / HoMi

Host-microbiome dual transcriptome pipeline
https://homi-pipeline.readthedocs.io
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Taxa barplot can't find pseq in prep_mdf #75

Closed sterrettJD closed 2 months ago

sterrettJD commented 2 months ago

Not sure why pseq can't be found. It definitely has already been defined

sterrettJD commented 2 months ago

error=T was set as a chunk param in the chunk responsible for loading the data correctly. This meant that when that chunk errored, the rest kept going.

It seems that the bugs list is getting ready incorrectly. Specifically, the colnames are incorrect. They're labeled as "V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" when they should be #clade_name NCBI_tax_id additional_species <sample IDs here >

sterrettJD commented 2 months ago

The issue is numeric sample IDs. Data.table looks the header row, which shouldn't contain numeric column names. Now, it's specified that the first row will be the header, as of https://github.com/sterrettJD/HoMi/commit/080d237a19781ae95099bf69b311e6c97b96533b