makeHeatmap: Plot allelic ratio as heatmap

In Wancen/airpart: Differential cell-type-specific allelic imbalance

Plot allelic ratio as heatmap

Description

Plot allelic ratio as heatmap

Usage

makeHeatmap(
  sce,
  assay = c("ratio_pseudo", "ratio", "counts"),
  genecluster = NULL,
  show_row_names = FALSE,
  order_by_group = TRUE,
  ...
)

Arguments

sce	SingleCellExperiment
assay	the assay to be plotted. Choices are "ratio_pseudo" which is the default, "ratio", "counts".
genecluster	an integer indicates which gene cluster heatmap want to be returned.
show_row_names	show row names or not
order_by_group	indicate whether order by group or order by cell types
...	Passsed on the other argument in Heatmap.

Value

generates a heatmap

Examples

set.seed(2021)
sce <- makeSimulatedData(p.vec = c(0.3, 0.5, 0.5, 0.3), ncl = 1)
sce <- preprocess(sce)
# display allelic ratio pattern in whole dataset
makeHeatmap(sce)

sce <- geneCluster(sce, G = seq_len(4), plot = FALSE)
sce_sub <- wilcoxExt(sce, genecluster = 1)
# display specific gene cluster partition result
makeHeatmap(sce_sub)
# display by cell type orders
makeHeatmap(sce_sub, order_by_group = FALSE)

Wancen/airpart documentation built on March 12, 2023, 11:53 a.m.