seuratComputeHeatmap {singleCellTK}R Documentation

seuratComputeHeatmap Computes the heatmap plot object from the pca slot in the input sce object

Description

seuratComputeHeatmap Computes the heatmap plot object from the pca slot in the input sce object

Usage

seuratComputeHeatmap(
  inSCE,
  useAssay,
  useReduction = c("pca", "ica"),
  dims = NULL,
  nfeatures = 30,
  fast = TRUE,
  combine = TRUE,
  raster = TRUE
)

Arguments

inSCE

(sce) object from which to compute heatmap (pca should be computed)

useAssay

Assay containing scaled counts to use in heatmap.

useReduction

Reduction method to use for computing clusters. One of "pca" or "ica". Default "pca".

dims

Number of components to generate heatmap plot objects. If NULL, a heatmap will be generated for all components. Default NULL.

nfeatures

Numer of features to include in the heatmap. Default 30.

fast

See DimHeatmap for more information. Default TRUE.

combine

See DimHeatmap for more information. Default TRUE.

raster

See DimHeatmap for more information. Default TRUE.

Value

plot object

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- seuratNormalizeData(sce, useAssay = "counts")
sce <- seuratFindHVG(sce, useAssay = "counts")
sce <- seuratScaleData(sce, useAssay = "counts")
sce <- seuratPCA(sce, useAssay = "counts")
heatmap <- seuratComputeHeatmap(sce, useAssay = "counts")
seuratHeatmapPlot(heatmap)

## End(Not run)
[Package singleCellTK version 2.0.0 Index]