PrepareHeatTreePlot: Function to plot heat tree

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

Function to plot heat tree

Description

This functions plots the heat tree.

Usage

PrepareHeatTreePlot(
  mbSetObj,
  meta,
  taxalvl,
  color,
  layoutOpt,
  comparison,
  wilcox.cutoff,
  switchCmpDirection,
  imgName,
  format = "png",
  dpi = 72
)

Arguments

mbSetObj	Input the name of the mbSetObj.
meta	Input the name of the group.
taxalvl	Character, input the taxonomic level to perform classification. For instance, "Genus" to use the Genus level.
color	Character, input the color palette code. "dbgr" for dark blue, grey and red. "bgy" for greenblue, grey and yellow. "ggr" for green, grey and red. "pgy" for purple, gray and yellow. "tgr" for teal, grey and red. "ggg" for green, grey and gold. Additionally, the viridis R package can be used to generate color schemes. "plasma" for the plasma color scheme, "viridis" for the default viridis color scheme and "cividis" for the cividis color scheme.
layoutOpt	Character, input the layout of the heat tree. "dft" for the default layout and "reda" for reingold-tilford.
comparison	Character, input the group comparisons.
wilcox.cutoff	Numeric, input the Wilcoxan p-value cutoff for significant node labels.
imgName	Character, input the name of the heat tree plot.
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 [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.