taxatree_funs: Create node and edge dataframes for taxatree_plots

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Create node and edge dataframes for taxatree_plots

Description

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.

Usage

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).

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.