AMPtk Downstream Tools¶
AMPtk to Phyloseq¶
Importing a BIOM table from AMPtk into Phyloseq is relatively straightforward:
#load in biom and tree file
physeq <- import_biom('mydata.biom', 'mydata.tree.phy')
#rename taxonomy headings
colnames(tax_table(physeq)) <- c("Kingdom", "Phylum", "Class",
"Order", "Family", "Genus", "Species")
#print the sample variables
sample_variables(physeq)
AMPtk to QIIME¶
The BIOM file produced by amptk taxonomy
is compatible directly with QIIME community ecology scripts, assuming that you have a QIIME compatible mapping file:
summarize_taxa_through_plots.py -i otu_table.biom -o taxa_summary -m mapping_file.txt