parseMetaphlanTSV: parseMetaphlanTSV

Description Usage Arguments Value Author(s)

View source: R/parser.R

Description

parse a MetaPhlan table to a tree object

Usage

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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 May 16, 2019, 8:12 p.m.