PerformBetaDiversity: Function to plot beta diversity.

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

Function to plot beta diversity.

Description

This functions creates beta diversity plots.

Usage

PerformBetaDiversity(
  mbSetObj,
  plotNm,
  ordmeth,
  distName,
  colopt,
  metadata,
  showlabel,
  taxrank,
  taxa,
  alphaopt,
  ellopt,
  comp.method,
  format = "png",
  dpi = 72,
  custom_col = "none",
  interactive = FALSE
)

Arguments

mbSetObj	Input the name of the mbSetObj.
plotNm	Character, input the name of the beta-diversity score plot.
ordmeth	Ordination method. Character, input "PCoA" to create a PCoA plot and "NMDS" to create a NMDS plot.
distName	Character, input the name of the distance method. "bray" for Bray-Curtis Index, "jsd" for Jensen-Shannon Divergence, "jaccard" for Jaccard Index, "unifrac" for Unweighted Unifrac Distance and "wunifrac" for Weighted Unifrac Distance.
colopt	Character, input whether the data points should be colored by experimental factor with "expfac", taxon abundance with "taxa" or alpha diversity with "alphadiv".
metadata	Input the name of the preferred experimental factor, only used if colopt is "expfac".
showlabel	Character, input whether or not to label samples in the plot. "none" to label no samples, "samnm" to label samples by their name, and "Class" for their group classification.
taxrank	Character, input the taxonomic level to calculate beta-diversity.
taxa	Character, input the specific taxon used to color the data points. Only used if colopt is set to "taxa".
alphaopt	Character, input the name of the alpha-diversity metric. "Chao1", "Observed", "ACE", "Shannon", "Simpson", or "Fisher".
ellopt	Character, input "yes" to show ellipses and "no" to not.
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.
custom_col	Set to "none" to use the default color palette, "viridis" to use the default viridis color palette, "plasma" to use the plasma viridis color palette and "magma" to use the magma color palette.
interactive	Boolean, if set to TRUE, saves the plot as an interactive html plot.

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.