signaturesHeatmap: signaturesHeatmap

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

signaturesHeatmap

Description

Heatmap containing the row normalised AUC values for the signatures in the topics.

Usage

signaturesHeatmap(
  object,
  topics = "all",
  selected.signatures = "all",
  nCores = 4,
  aucMaxRank = 0.03 * nrow(aucellRankings),
  col.low = "dodgerblue",
  col.mid = "floralwhite",
  col.high = "brown1",
  scale = TRUE,
  transposeHeatmap = FALSE,
  ...
)

Arguments

object	Initialized cisTopic object, after regions scores have been calculated with getRegionScores and object@signatures is filled.
topics	By default all topics will be used, but topics can be selected based on index.
selected.signatures	By default all signatures will be used, but signatures can be selected based on index or name. Alternatively, 'annotation' can be selected to use as signatures the region type labels (e.g. promoter, distal intergenic, ...) For this, the function annotateRegions() must be run first.
nCores	Number of cores to be used for AUCell
aucMaxRank	Threshold to calculate the AUC
col.low	Color to use for lowest signature enrichment
col.mid	Color to use for medium signature enrichment
col.high	Color to use for high signature enrichment
scale	Whether AUC enrichment should be normalized
transposeHeatmap	Transposes the heatmap (e.g. Topics as rows instead of columns)
...	See Heatmap from ComplexHeatmap

Value

Heatmap showing the enrichment per topic per signature

Examples

###
# Load cisTopic object:
path2cisTopicObject <- system.file(package="cisTopic", "examples/cisTopicObject_melanoma.Rds")
cisTopicObject <- readRDS(path2cisTopicObject)
###

signaturesHeatmap(cisTopicObject)

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