ann_tree: Annotate a tree
In pctax: Professional Comprehensive Omics Data Analysis

ann_tree

R Documentation

Annotate a tree

Description

Annotate a tree

Easy way to plot a phylogenetic tree

Usage

ann_tree(f_tax, otutab = NULL, level = ncol(f_tax))

easy_tree(
  tree,
  highlight = "Phylum",
  colorfill = "color",
  pal = NULL,
  name_prefix = FALSE,
  basic_params = NULL,
  add_abundance = TRUE,
  color_name = "abundance",
  add_tiplab = TRUE,
  fontsize = NULL
)

Arguments

`f_tax`	taxonomy dataframe
`otutab`	otutab, rowname==rowname(taxonomy)
`level`	1~7
`tree`	result from `ann_tree`
`highlight`	highlight which level, one of `tree$level`
`colorfill`	"color" or "fill"
`pal`	color pal
`name_prefix`	keep the prefix like "k__" or "p__" in the label? Default: FALSE
`basic_params`	parameters parse to `ggtree`
`add_abundance`	logical
`color_name`	color name
`add_tiplab`	logical
`fontsize`	tip label fontsize

Value

a treedata

a ggplot

Examples

if (interactive()) {
  data(otutab, package = "pcutils")
  ann_tree(taxonomy, otutab) -> tree
  # run yourself
  easy_tree(tree, add_abundance = FALSE) -> p
  p
}

pctax documentation built on May 29, 2024, 10:03 a.m.