PlotOverallPieGraph: Main function to plot pie graphs of microbiome data.

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Main function to plot pie graphs of microbiome data.

Description

This functions plots pie graphs of microbiome data. In particular, it plots the overall pie chart (all samples). The data used to calculate the pie-chart is saved in your working directory as ""piechart_abundances.csv".

Usage

PlotOverallPieGraph(
  mbSetObj,
  taxalvl,
  feat_cnt,
  calcmeth,
  toptaxapie,
  pietoptaxaopt
)

Arguments

mbSetObj	Input the name of the mbSetObj.
taxalvl	Character, input the taxonomic level to perform classification. For instance, "Genus" to use the Genus level.
feat_cnt	Set the minimum feature count that is used to "bin" together small taxa.
calcmeth	Merge small taxa based on the sum /("sum"/) or median /("med"/) counts across all samples or groups.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.