vdjHeatmap: Heatmap of cells with VDJ recombination

In SingerLab/gac: Genetic Analysis of Cells

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",
  col = NULL,
  cell.type.colors = NULL,
  chromosome.colors = NULL,
  gene.type.colors = NULL,
  ...
)

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
col	copy number colors, default is NULL and will generate a black, white and red color palette.
cell.type.colors	color map for cell types. default is NULL
chromosome.colors	color map for VDJ chromosomes. default is NULL
gene.type.colors	color map for VDJ Gene types. default is NULL
...	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 March 23, 2024, 5:15 a.m.