I am running beta_diversity_through_plots.py to produce a PCoA plot as follows:
beta_diversity_through_plots.py -i nps_only.biom -m ../../mapping_files/mapfile_Runs1234_extra.txt -o beta_nps_raw_extra -t ../rep_set.tre --color_by_all_fields
One of the columns in my mapping file is 'depth', which contains the sequencing depth of each sample. I am trying to colour the plot in Emperor by depth just to check that there's no clustering by sequencing depth. However, depth does not appear as an option in the drop-down menu for colouring by metadata. All other columns from the mapping file are present. I thought it may be because the values are numeric, but I have had success using a mapping file generated from summarize_taxa.py that adds the taxonomic information to the file, allowing me to gradient colour by taxon abundance (also numeric).
I have attached the mapping file, biom table and phylogenetic tree I am using. I get no errors or warnings when validating the mapping file.
Can anyone help me fix this issue? I just can't work it out!