cellTopicHeatmap: Cell-cisTopic distribution heatmap

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

Cell-cisTopic distribution heatmap

Description

Plot cell states based on dimensionality reduction over cell-cisTopic distributions

Usage

cellTopicHeatmap(
  object,
  method = "Z-score",
  colorBy = NULL,
  colVars = NULL,
  col.low = "floralwhite",
  col.mid = "pink",
  col.high = "red",
  select.cells = NULL,
  ...
)

Arguments

object	Initialized cisTopic object, after the [e-mail] has been filled.
method	Select the normalization method to use for plotting: 'Z-score' or 'Probability'.
colorBy	Select the cell metadata used to colour the plots with. By default, all categorical features are used.
colVars	List specifying the colors to use for each label in each colouring level
col.low	Color to use for lowest topic enrichment
col.mid	Color to use for medium topic enrichment
col.high	Color to use for high topic enrichment
select.cells	If a subset of cells want to be used for making the heatmap, selected cell names can be provided (as a vector).
...	See Heatmap from ComplexHeatmap

Details

'Z-score' computes the Z-score for each topic assingment per cell/region and 'Probability' divides the topic assignments by the total number of assignments in the cell/region in the last iteration plus alpha.

Value

Heatmap clustering cells based on their cell-cisTopic distributions.

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.