This was mostly my pilot work, making sure I understand how to work with phyloseq/findPhyseqData(). Instead of working with "batch" and "condition" vectors, we get to work with the whole sample_data() matrix, letting users pick primary and secondary covariates. I have not yet changed the differential expression analyses. This change only works when paired with certain changes to ui.R
This was mostly my pilot work, making sure I understand how to work with phyloseq/findPhyseqData(). Instead of working with "batch" and "condition" vectors, we get to work with the whole sample_data() matrix, letting users pick primary and secondary covariates. I have not yet changed the differential expression analyses. This change only works when paired with certain changes to ui.R