Seurat
but
plots the heatmap using ComplexHeatmap
and cowplot
libraries.R/computeHeatmap.R
computeHeatmap.Rd
computeHeatmap
The computeHeatmap method computes the heatmap visualization for a set
of features against a set of dimensionality reduction components. This
method uses the heatmap computation algorithm code from Seurat
but
plots the heatmap using ComplexHeatmap
and cowplot
libraries.
computeHeatmap(
inSCE,
useAssay,
dims = 10,
nfeatures = 30,
cells = NULL,
reduction = "pca",
disp.min = -2.5,
disp.max = 2.5,
balanced = TRUE,
nCol = NULL,
externalReduction = NULL
)
Input SingleCellExperiment
object.
The assay to use for heatmap computation.
Specify the number of dimensions to use for heatmap. Default
10
.
Specify the number of features to use for heatmap. Default
is 30
.
Specify the samples/cells to use for heatmap computation.
Default is NULL
which will utilize all samples in the assay.
Specify the reduction slot in the input object. Default
is "pca"
.
Specify the minimum dispersion value to use for floor
clipping of assay values. Default is -2.5
.
Specify the maximum dispersion value to use for ceiling
clipping of assay values. Default is 2.5
.
Specify if the number of of up-regulated and down-regulated
features should be balanced. Default is TRUE
.
Specify the number of columns in the output plot. Default
is NULL
which will auto-compute the number of columns.
Specify an external reduction if not present in
the input object. This external reduction should be created
using CreateDimReducObject
function.
Heatmap plot object.