PlotLEfSeSummary: Plot LEfSe summary

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

Plot LEfSe summary

Description

This functions graphically summarizes the LEfSe results in a VIP plot.

Usage

PlotLEfSeSummary(
  mbSetObj,
  ldaFeature,
  layoutOptlf,
  imgName,
  format = "png",
  width = NA,
  dpi = 72,
  colOpt = "default"
)

Arguments

mbSetObj	Input the name of the mbSetObj.
ldaFeature	Numeric, input the number of top features to include in the plot.
layoutOptlf	Character, input "dot" to create the VIP plot and "bar" to create the bar graph.
imgName	Character, input the name of the plot.
format	Character, input the preferred format of the plot. By default it is set to "png".
width	Numeric, input the width of the plot. By default it is set to NA.
dpi	Numeric, input the dots per inch. By default it is set to 72.
colOpt	Character, "default", "viridis", "cividis", or "plasma".

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.