parseMetaphlanTSV: parseMetaphlanTSV

In lch14forever/microbiomeViz:

Description

parse a MetaPhlan table to a tree object

Usage

parseMetaphlanTSV(
  tax.profile,
  index = 1,
  header = FALSE,
  delimiter = "\\|",
  node.size.scale = 1,
  node.size.offset = 1
)

Arguments

tax.profile	a single metaphlan table (either a file path or a a data.frame)
index	the column number of taxonomic annotation
header	whether tax.profile provided as a file path contains a header
delimiter	delimiter to separate taxonomic anotations
node.size.scale	the parameter 'a' controlling node size: nodeSize=a*log(relative_abundance)+b
node.size.offset	the parameter 'b' controlling node size: nodeSize=a*log(relative_abundance)+b

Value

a treeio::treedata object

Author(s)

Chenhao Li, Guangchuang Yu

lch14forever/microbiomeViz documentation built on Sept. 7, 2020, 4:34 p.m.