PlotHeatmap: Main function to plot heatmap.

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

Main function to plot heatmap.

Description

This functions plots a heatmap from the mbSetObj.

Usage

PlotHeatmap(
  mbSetObj,
  plotNm,
  dataOpt = "norm",
  scaleOpt = "row",
  smplDist,
  clstDist,
  palette,
  metadata,
  taxrank,
  viewOpt,
  doclust,
  format = "png",
  colname,
  rowname,
  fontsize_col,
  fontsize_row,
  annoPer,
  fzAnno,
  appendnm = "F",
  rowV = F,
  colV = T,
  var.inx = NA,
  border = T,
  width = NA,
  dpi = 72
)

Arguments

mbSetObj	Input the name of the mbSetObj.
plotNm	Character, input the name of the plot.
smplDist	Input the distance measure. "euclidean" for Euclidean distance, "correlation" for Pearson, and "minkowski" for Minkowski.
clstDist	Character, input the name of the selected clustering algorithm. "ward" for Ward, "average" for Average, "complete" for Complete, and "single" for Single.
palette	Set the colors of the heatmap. By default it is set to "bwm", blue, white, to red. Use "gbr" for green, black, red, use "heat" for red to yellow, "topo" for blue to yellow, "gray" for white to black, and "byr" for blue, yellow, red.
metadata	Character, input the name of the experimental factor to cluster samples by.
taxrank	Character, input the taxonomic level to perform classification. For instance, "OTU-level" to use OTUs.
viewOpt	Character, "overview" to view an overview of the heatmap, and "detail" to iew a detailed view of the heatmap (< 1500 features).
doclust	Logicial, default set to "F".
format	Character, input the preferred format of the plot. By default it is set to "png".
colname	Logical, specify the if column name is shown, default set to "T",
rowname	Logical, specify the if row name is shown, default set to "T",
fontsize_col	Numeric, fontsize for colnames
fontsize_row	Numeric, fontsize for rownames
appendnm	Logical, "T" to prepend higher taxon names.
rowV	Logical, default set to "F".
colV	Logical, default set to "T".
var.inx	Default set to NA.
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.

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.