produce a heatmap from a specialized CITE-seq SingleCellExperiment

Source: R/adt_profiles.R

produce a heatmap from a specialized CITE-seq SingleCellExperiment

adtProfiles(x, lb = -3, ub = 3, do_z = FALSE)

Arguments

x

SingleCellExperiment instance that has an `se.averaged` component in its metadata

lb

numeric(1) lower bound on 'breaks' sequence for ComplexHeatmap::pheatmap, defaults to -3

ub

numeric(1) upper bound on 'breaks' sequence for ComplexHeatmap::pheatmap, defaults to 3

do_z

logical(1) if TRUE, divide the residuals by their standard deviation across clusters, defaults to false

Value

ComplexHeatmap::pheatmap instance

side effect of pheatmap::pheatmap call

Note

See the OSCA book ch12.5.2 for the application.

Examples

ch12sce <- getCh12Sce()
adtProfiles(ch12sce)

adtProfiles(ch12sce, do_z = TRUE)