seuratComputeHeatmap: seuratComputeHeatmap Computes the heatmap plot object from...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.