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

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

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

Description

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

Usage

runSeuratHeatmap(
  inSCE,
  useAssay,
  useReduction = c("pca", "ica"),
  dims = NULL,
  nfeatures = 30,
  cells = NULL,
  ncol = NULL,
  balanced = TRUE,
  fast = TRUE,
  combine = TRUE,
  raster = TRUE,
  externalReduction = NULL
)

Arguments

inSCE	(sce) object from which to compute heatmap (pca should be computed)
useAssay	Specify name of the assay that will be scaled by this function. The output scaled assay will be used for computation of the 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	Number of features to include in the heatmap. Default 30.
cells	Numeric value indicating the number of top cells to plot. Default is NULL which indicates all cells.
ncol	Numeric value indicating the number of columns to use for plot. Default is NULL which will automatically compute accordingly.
balanced	Plot equal number of genes with positive and negative scores. Default is TRUE.
fast	See DimHeatmap for more information. Default TRUE.
combine	See DimHeatmap for more information. Default TRUE.
raster	See DimHeatmap for more information. Default TRUE.
externalReduction	Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

Value

plot object

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
heatmap <- runSeuratHeatmap(sce, useAssay = "counts")
plotSeuratHeatmap(heatmap)

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.