vdjHeatmap: Heatmap of cells with VDJ recombination

View source: R/vdjHeatmap.R

vdjHeatmapR Documentation

Heatmap of cells with VDJ recombination

Description

Heatmap of cells with VDJ recombination

Usage

vdjHeatmap(
  cnr,
  vdj.genes = NULL,
  vdjGeneAnno = NULL,
  vdjCellAnno = NULL,
  gene.type.column = "gene_biotype",
  ...
)

Arguments

cnr

a cnir bundle

vdj.genes

list of VDJ genes. By default is set to NULL, vdj.genes is the union of T-cell Receptor and B-cell Receptor genes (i.e. TR, IG genes, used in genotype_vdj)

vdjGeneAnno

HeatmapAnnotation object to annotate gene attributes

vdjCellAnno

rowAnnotation object to annotate cells

gene.type.column

name of column with gene type, default "gene_biotype

...

additional arguments passed to ComplexHeatmap::Heatmap

Value

Returns a heatmap of VDJ cells with rows as cells, and TR/IG genes as columns. Heatmap is split by chromosome name, and cell types are annotated on the left

Examples

data(cnr)

cnr <- genotype_vdj(cnr)

vdjHeatmap(cnr)


SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.