PlotAlphaData: Function to plot alpha-diversity analysis.

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

Function to plot alpha-diversity analysis.

Description

This functions creates a plot for alpha-diversity.

Usage

PlotAlphaData(
  mbSetObj,
  data.src,
  bargraphName,
  distName,
  metadata,
  taxrank,
  colors = "default",
  format = "png",
  dpi = 72,
  interactive = FALSE
)

Arguments

mbSetObj	Input the name of the mbSetObj.
data.src	Character, input whether alpha diversity is calculated using the filtered /("filt"/) or raw data /("orig"/).
bargraphName	Character, input the name of the plot.
distName	Character, input the diversity measure to calculate alpha-diversity. "Chao1", "Observed", "ACE", "Shannon", "Simpson", or "Fisher".
metadata	Character, input the name of the experimental factor to group the samples.
taxrank	Character, input the taxonomic level to calculate alpha-diversity. "Phylum", "Class", "Order", "Family", "Genus", "Species" or "OTU".
colors	Character, set to "default" to use the default colors, "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.
group	Boolean, input whether or not to group the samples in the dot plot. 0 or 1.

Author(s)

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

xia-lab/MicrobiomeAnalystR documentation built on Feb. 24, 2025, 5:36 a.m.