PlotTaxaAundanceBar: Function to plot bar charts for alpha diversity

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

Function to plot bar charts for alpha diversity

Description

This functions plots bar charts of different taxonomic levels for alpha diversity.

Usage

PlotTaxaAundanceBar(
  mbSetObj,
  barplotName,
  taxalvl,
  facet,
  facet2,
  imgOpt,
  feat_cnt,
  colpalopt,
  calcmeth,
  toptaxa,
  abunTopTaxaOpt,
  appendnm,
  format = "png",
  dpi = 72,
  interactive = FALSE
)

Arguments

mbSetObj	Input the name of the mbSetObj.
barplotName	Character, input the name of the barplot.
taxalvl	Character, input the taxonomic level to perform classification. For instance, "Genus" to use the Genus level.
facet	Character, set the group to separate the bar plots.
imgOpt	Character, set the graph type. Stacked bar using the actual abundance, use "barraw". Stacked bar using the percentage abundance, use "barnorm".
feat_cnt	Set the minimum feature count that is used to "bin" together small taxa.
colpalopt	Select the color palette options. "set3", which is the Set3 from the R Color Brewer, "cont21" which is a set of 21 colors, "cont28" which is a set of 28 colors, and "cont42" which is a set of 42 colors. For users who wish to use a color palette robust to colorblindness /(https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html/), use "viridis", "magma", "plasma", or "inferno".
calcmeth	Merge small taxa based on the sum /("sum"/) or median /("med"/) counts across all samples or groups.
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 TRUE, will save an interactive version of the Stacked Bar plot using plotly.
metadata	If users wish to merge samples to groups in the stacked bar plot, set this to the preferred grouping.

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.