R/seuratFunctions.R
runSeuratHeatmap.Rd
runSeuratHeatmap Computes the heatmap plot object from the pca slot in the input sce object
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
)
(sce) object from which to compute heatmap (pca should be computed)
Assay containing scaled counts to use in heatmap.
Reduction method to use for computing clusters. One of
"pca" or "ica". Default "pca"
.
Number of components to generate heatmap plot objects. If
NULL
, a heatmap will be generated for all components. Default
NULL
.
Number of features to include in the heatmap. Default
30
.
Numeric value indicating the number of top cells to plot.
Default is NULL
which indicates all cells.
Numeric value indicating the number of columns to use for plot.
Default is NULL
which will automatically compute accordingly.
Plot equal number of genes with positive and negative scores.
Default is TRUE
.
See DimHeatmap for more information. Default
TRUE
.
See DimHeatmap for more information. Default
TRUE
.
See DimHeatmap for more information. Default
TRUE
.
Pass DimReduc object if PCA/ICA computed through
other libraries. Default NULL
.
plot object
data(scExample, package = "singleCellTK")
if (FALSE) {
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)
}