CoreMicrobeAnalysis: Perform core microbiome analysis

Description Usage Arguments Author(s)

View source: R/mdp_utils.R

Description

This functions performs core microbiome analysis.

Usage

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

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.

detection

Numeric, input the relative abundance cutoff.

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.

Author(s)

Jeff Xia [email protected] McGill University, Canada License: GNU GPL (>= 2)


xia-lab/MicrobiomeAnalystR documentation built on Oct. 17, 2019, 9:05 a.m.