CoreMicrobeAnalysis: Perform core microbiome analysis

View source: R/mdp_utils.R

CoreMicrobeAnalysisR Documentation

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 jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)


xia-lab/MicrobiomeAnalystR documentation built on Sept. 7, 2024, 1:26 p.m.