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.