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 )
inSCE | Input |
---|---|
useAssay | The assay to use for heatmap computation. |
dims | Specify the number of dimensions to use for heatmap. Default
|
nfeatures | Specify the number of features to use for heatmap. Default
is |
cells | Specify the samples/cells to use for heatmap computation.
Default is |
reduction | Specify the reduction slot in the input object. Default
is |
disp.min | Specify the minimum dispersion value to use for floor
clipping of assay values. Default is |
disp.max | Specify the maximum dispersion value to use for ceiling
clipping of assay values. Default is |
balanced | Specify if the number of of up-regulated and down-regulated
features should be balanced. Default is |
nCol | Specify the number of columns in the output plot. Default
is |
externalReduction | Specify an external reduction if not present in
the input object. This external reduction should be created
using |
Heatmap plot object.