taxon_sort_gather: Transform data from wide to long, join a taxonomic level,...
In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Transform data from wide to long, join a taxonomic level, aggregate and create summary statistics, and return n OTUs.

taxon_sort_gather(
  df,
  n = 50,
  facet_var = NULL,
  ord_val = NULL,
  tax_df = otu_good_taxonomy,
  tax_level = "Phylum"
)

`df`	Dataframe containing metadata and taxon (Phylum, Otu, etc) abundance data in wide format.
`n`	Number of OTUs to return, 50 by default. Fewer results will be returned if there are not enough entities with non-zero abundances.
`facet_var`	Variable to be used for grouping and eventual faceting, possibly in `plot_ra`.
`ord_val`	Level with the `facet_var` to be used for ranking OTUs.
`tax_df`	Taxonomy table. Passed to `join_tax`. Defaults to `otu_good_taxonomy`.
`tax_level`	Taxonomic level to join from `tax_df`, the levels within which will be used for grouping. Defaults to Phylum.

A dataframe that has been aggregated and reshaped into long form.

1 2	filt_ord_facet_df <- dplyr::filter(otu_good_14d, Day == 0, Organ == "Feces") %>% taxon_sort_gather(facet_var = "Treatment_group", ord_val = "untreated", tax_level = "Phylum")