Create node and edge dataframes for taxatree_plots

Source: R/taxatree_funs.R

Mostly you will not have to use these functions directly: instead call taxatree_plots with the output of taxatree_stats

  • taxatree_nodes creates taxon nodes and calculates a summary statistic about each taxon (given by fun). Takes a psExtra or phyloseq object.

  • taxatree_edges uses the output of taxatree_nodes to create a dataframe of edges.

taxatree_nodes(
  ps,
  fun = list(sum = sum),
  ranks = "all",
  .sort = NULL,
  .use_counts = TRUE
)

taxatree_edges(nodes_df)

Arguments

ps

phyloseq object or psExtra

fun

function to calculate for each taxon/node

ranks

selection of taxonomic ranks to make nodes for ("all", or names)

.sort

sort nodes by "increasing" or "decreasing" values of fun function result

.use_counts

use count data if available (instead of transformed data)

nodes_df

dataframe output from taxatree_nodes

Details

taxatree_nodes makes nodes for taxa at all ranks or for a list of consecutive ranks (plus a root rank if tree is not rooted).