modCorPlot {tmod}

Plot a correlation heatmap for modules

Description

Plot a correlation heatmap for modules

Usage

modCorPlot(
  modules,
  mset = NULL,
  heatmap_func = pheatmap,
  labels = NULL,
  stat = "jaccard",
  upper.cutoff = NULL,
  ...
)

Arguments

modules

either a character vector with module IDs from mset, or a list which contains the module members

mset

Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)

heatmap_func

function drawing the heatmap

labels

Labels for the modules (if NULL, labels will be retrieved from 'mset')

stat

Type of statistics to return. "jaccard": Jaccard index (default); "number": number of common genes; "soerensen": Soerensen-Dice coefficient; "overlap": Szymkiewicz-Simpson coefficient.

upper.cutoff

Specify upper cutoff for the color palette

...

Any further parameters are passed to the heatmap function (by default, [pheatmap()].

Value

Returns the return value of heatmap_func (by default, a pheatmap object).