celdaHeatmap: Plot celda Heatmap

In campbio/celda: CEllular Latent Dirichlet Allocation

Plot celda Heatmap

Description

Render a stylable heatmap of count data based on celda clustering results.

Usage

celdaHeatmap(
  sce,
  useAssay = "counts",
  altExpName = "featureSubset",
  featureIx = NULL,
  nfeatures = 25,
  ...
)

## S4 method for signature 'SingleCellExperiment'
celdaHeatmap(
  sce,
  useAssay = "counts",
  altExpName = "featureSubset",
  featureIx = NULL,
  nfeatures = 25,
  ...
)

Arguments

sce	A SingleCellExperiment object returned by celda_C, celda_G, or celda_CG.
useAssay	A string specifying which assay slot to use. Default "counts".
altExpName	The name for the altExp slot to use. Default "featureSubset".
featureIx	Integer vector. Select features for display in heatmap. If NULL, no subsetting will be performed. Default NULL. Only used for sce containing celda_C model result returned by celda_C.
nfeatures	Integer. Maximum number of features to select for each gene module. Default 25. Only used for sce containing celda_CG or celda_G model results returned by celda_CG or celda_G.
...	Additional parameters passed to plotHeatmap.

Value

list A list containing dendrogram information and the heatmap grob

See Also

'celdaTsne()' for generating 2-dimensional tSNE coordinates

Examples

data(sceCeldaCG)
celdaHeatmap(sceCeldaCG)

campbio/celda documentation built on April 5, 2024, 11:47 a.m.