prep_func_node_info {POMS}

Get node indices of FSN and BSN categories across tree for a given function

Description

Parse POMS_pipeline output to look at FSNs for a specific function (e.g., a specific gene family). Will also parse BSN information (which is not dependent on a particular function). This is convenient to do before plotting the distribution of FSNs and BSNs across the tree with the ggtree R package for instance. When a taxa label table is specified, labels of tested nodes in the tree (found in the POMS_pipeline output object) will be renamed to be the representative taxa on each side.

Usage

prep_func_node_info(
  POMS_output,
  func_id,
  taxa_table = NULL,
  taxa_threshold = 0.75,
  full_taxon_label = FALSE
)

Arguments

POMS_output

output object from POMS_pipeline function.

func_id

label of function for which should FSNs should be parsed. Must be present in POMS_output$FSNs_summary.

taxa_table

optional dataframe containing taxa labels for each tip of tree. Must be in same format as expected for node_taxa function.

taxa_threshold

float > 0.5 and <= 1.0 specifying the proportion of tips that must share a taxon label for it to be considered representative. Only relevant if taxa_table specified.

full_taxon_label

boolean flag for whether taxon labels should be combined, so that all higher taxonomic labels are included. Specifically, when TRUE, all higher labels are concatenated and delimited by "; ". E.g., rather than just the genus "Odoribacter" the label would be "Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Odoribacter". Only relevant if taxa_table specified.

Value

List containing final tree as well as indices of nodes corresponding to different FSN and BSN categories. If taxa_table was specified, then node labels in tree will correspond to representative taxa on each side of the nodes that were tested (i.e., those that were non-negligible).