PlotAlphaBoxData: Function to create box plots for alpha diversity analysis

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

Function to create box plots for alpha diversity analysis

Description

This functions performs metagenome seq analysis on the microbiome data.

Usage

PlotAlphaBoxData(
  mbSetObj,
  boxplotName,
  distName,
  metadata,
  colors = "default",
  format = "png",
  dpi = 72
)

Arguments

mbSetObj	Input the name of the mbSetObj.
boxplotName	Character, input the name of the boxplot.
distName	Character, input the diversity measure to calculate alpha-diversity. "Chao1", "Observed", "ACE", "Shannon", "Simpson", or "Fisher".
metadata	Input the name of the experimental factor to group the samples.
colors	Use "default", "viridis" to use the viridis color palette, "plasma" to use the plasma color palette, "magma" to use the magma color palette, or "magma" to use the magma color palette.
format	Character, input the preferred format of the plot. By default it is set to "png".
dpi	Numeric, input the dots per inch. By default it is set to 72.

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.