CoreMicrobeAnalysis: Perform core microbiome analysis

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

Perform core microbiome analysis

Description

This functions performs core microbiome analysis.

Usage

CoreMicrobeAnalysis(
  mbSetObj,
  imgName,
  preval,
  detection,
  taxrank,
  palette,
  viewOpt,
  analOpt,
  expFact,
  group,
  format = "png",
  dpi = 72,
  width = NA,
  interactive = FALSE
)

Arguments

mbSetObj	Input the name of the mbSetObj.
imgName	Input the name of the core microbiome analysis plot.
preval	Numeric, input the sample prevalence cutoff. This is the minimum number of samples that share this microbe.
detection	Numeric, input the relative abundance cutoff. This is the minimum detection threshold of X percent relative abundance.
palette	Character, input the color palette. "bwm" for the default color palette /(blue, white, red/), "gbr" for the red and green color palette, "heat" for the yellow to red color palette, "topo" for the blue, green, and yellow color palette, "gray" for the gray color palette, "byr" for the blue, yellow and red color palette, "viridis" for the viridis default color palette and "plasma" for the plasma viridis 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.
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 Sept. 7, 2024, 1:26 p.m.