PlotTreeGraph: Function to plot tree graphics for dendogram.

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

Function to plot tree graphics for dendogram.

Description

This functions creates dendogram tree plots.

Usage

PlotTreeGraph(
  mbSetObj,
  plotNm,
  distnm,
  clstDist,
  metadata,
  taxrank,
  colorOpts,
  format = "png",
  dpi = 72,
  width = NA,
  plotType = "rectangle"
)

Arguments

mbSetObj	Input the name of the mbSetObj.
plotNm	Character, input the name of the plot.
distnm	Character, input the name of the selected distance measure. "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.
clstDist	Character, input the name of the selected clustering algorithm. "ward" for Ward, "average" for Average, "complete" for Complete, and "single" for Single.
metadata	Character, input the name of the experimental factor.
taxrank	Character, input the taxonomic level to perform classification. For instance, "OTU-level" to use OTUs.
colorOpts	Character, "default" or "viridis".
format	Character, by default the plot is .png format.
dpi	The dots per inch. Numeric, by default it is set to 72.
width	Width of the plot. Numeric, by default it is set to NA.
plotType	Character, default is set to "rectangle". Alternative is "triangle".
datatype	Character, "16S" if marker gene data and "metageno" if shotgun 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.