microbeHeatmap: Plot microbe co-occurrence in a heatmap

In waldronlab/BugSigDBStats: BugSigDB Stats and Analysis

Plot microbe co-occurrence in a heatmap

Description

Plot microbe co-occurrence in a heatmap

Usage

microbeHeatmap(
  dat,
  sig.type = c("both", "increased", "decreased"),
  tax.level = "mixed",
  exact.tax.level = FALSE,
  antagonistic = FALSE,
  anno = "phylum",
  top = 100,
  fontsize = 6,
  ...
)

Arguments

dat	a data.frame storing BugSigDB data.
sig.type	character. Signature type. Use either "increased" or "decreased" to subset to signatures with either increased or decreased abundance in the exposed group, respectively. Default is "both" which will not subset by the direction of abundance change.
tax.level	character. Either "mixed" or any subset of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain"). This full vector is equivalent to "mixed".
exact.tax.level	logical. Should only the exact taxonomic level specified by tax.level be returned? Defaults to TRUE. If FALSE, a more general tax.level is extracted for microbes given at a more specific taxonomic level.
antagonistic	logical. Antagonistic co-occurrence, ie occurring together but one microbe up the other one is down? Defaults to FALSE.
anno	character. Taxonomic level that should be displayed as an annotation bar. Defaults to "phylum".
top	integer. The number of microbes to display. Defaults to 100.
fontsize	integer. Fontsize for text. Defaults to 6.
...	additional arguments to ComplexHeatmap::Heatmap.

Value

Plots to a graphics device. Returns the co-oocurence matrix invisibly.

waldronlab/BugSigDBStats documentation built on Oct. 15, 2024, 5:16 p.m.