feat_heatmap: Create a heatmap of features organized by cluster
In Chris-Cherry/domino: Receptor Ligand Analysis for Single Cell RNA Seq

feat_heatmap

R Documentation

Create a heatmap of features organized by cluster

Description

Creates a heatmap of feature expression (typically transcription factor activation scores) by cells organized by cluster.

Usage

feat_heatmap(
  dom,
  feats = NULL,
  bool = TRUE,
  bool_thresh = 0.2,
  title = TRUE,
  norm = FALSE,
  cols = NULL,
  ann_cols = TRUE,
  min_thresh = NULL,
  max_thresh = NULL,
  ...
)

Arguments

`dom`	A domino object with network built (build_domino)
`feats`	Either a vector of features to include in the heatmap or 'all' for all features. If left NULL then the features selected for the signaling network will be shown.
`bool`	A boolean indicating whether the heatmap should be continuous or boolean. If boolean then bool_thresh will be used to determine how to define activity as positive or negative.
`bool_thresh`	A numeric indicating the threshold separating 'on' or 'off' for feature activity if making a boolean heatmap.
`title`	Either a string to use as the title or a boolean describing whether to include a title. In order to pass the 'main' parameter to NMF::aheatmap you must set title to FALSE.
`norm`	Boolean indicating whether or not to normalize the transcrption factors to their max value.
`cols`	A named vector of colors to annotate cells by cluster color. Values are taken as colors and names as cluster. If left as NULL then default ggplot colors will be generated.
`ann_cols`	Boolean indicating whether to include cell cluster as a column annotation. Colors can be defined with cols. If FALSE then custom annotations can be passed to NMF.
`min_thresh`	Minimum threshold for color scaling if not a boolean heatmap
`max_thresh`	Maximum threshold for color scaling if not a boolean heatmap
`...`	Other parameters to pass to NMF::aheatmap. Note that to use the 'main' parameter of NMF::aheatmap you must set title = FALSE and to use 'annCol' or 'annColors' ann_cols must be FALSE.