PCoA3D.Anal: Main function to perform PCoA analysis

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

Main function to perform PCoA analysis

Description

This functions creates a 3D PCoA plot from the microbiome data. This is used by the Beta-Diversity analysis. The 3D interactive visualization is on the web.

Usage

PCoA3D.Anal(
  mbSetObj,
  ordMeth,
  distName,
  taxrank,
  colopt,
  variable,
  taxa,
  alphaopt,
  jsonNm
)

Arguments

mbSetObj	Input the name of the mbSetObj.
ordMeth	Character, input the name of the ordination method. "PCoA" for principal coordinate analysis and "NMDS" for non-metric multidimensional scaling.
distName	Character, input the name of the distance method.
taxrank	Character, input the taxonomic level for beta-diversity analysis.
colopt	Character, color the data points by the experimental factor, the taxon abundance of a selected taxa, or alpha diversity.
variable	Character, input the name of the experimental factor.
taxa	Character, if the data points are colored by taxon abundance, input the name of the selected taxa.
alphaopt	Character, if the data points are colored by alpha-diversity, input the preferred alpha-diversity measure.
jsonNm	Character, input the name of the json file to output.
datatype	Character, input "16S" if the data is marker gene data and "metageno" if it is metagenomic data.

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.