vdjHeatmap | R Documentation |
Heatmap of cells with VDJ recombination
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,
...
)
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 |
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
data(cnr)
cnr <- genotype_vdj(cnr)
vdjHeatmap(cnr)
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