Transform a taxonomy annotate data frame into an upset plot compliant data frame

`from_taxonomy_annotate_to_upset_inputs()` transforms a data frame with produced using read_taxonomy_annotate on many results produced by sourmash taxonomy annotate into a upset-compliant data frame. The function can optionally agglomerate to different levels of taxonomic rank (e.g. phylum) and then produce the upset compliant data frame after agglomeration.

Usage

from_taxonomy_annotate_to_upset_inputs(
  taxonomy_annotate_df,
  tax_glom_level = NULL
)

Arguments

taxonomy_annotate_df

Data frame containing outputs from sourmash taxonomy annotate. Can contain results from one or many runs of sourmash taxonomy annotate. Agglomeration occurs within each query.

tax_glom_level

Optional character string specifying the taxonomic rank to agglomerate k-mer counts. Must be one of "domain", "phylum", "class", "order", "family", "genus", "species."

Value

A list. The first object in the list is an upset compliant data frame. The second is the taxonomy_annotate_df used to build the upset data frame. The last is the tax_glom_level.

Examples

if (FALSE) {
from_taxonomy_annotate_to_upset_inputs()
}