seuratComputeHeatmap {singleCellTK} | R Documentation |
seuratComputeHeatmap Computes the heatmap plot object from the pca slot in the input sce object
seuratComputeHeatmap( inSCE, useAssay, useReduction = c("pca", "ica"), dims = NULL, nfeatures = 30, fast = TRUE, combine = TRUE, raster = TRUE )
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 |
dims |
Number of components to generate heatmap plot objects. If |
nfeatures |
Numer of features to include in the heatmap. Default |
fast |
See DimHeatmap for more information. Default |
combine |
See DimHeatmap for more information. Default |
raster |
See DimHeatmap for more information. Default |
plot object
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)