percentGenes: Examining the VDJ gene usage across clones

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Examining the VDJ gene usage across clones

Description

This function the proportion V or J genes used by grouping variables. This function only quantifies single gene loci for indicated chain. For examining VJ pairing, please see codepercentVJ

Usage

percentGenes(
  input.data,
  chain = "TRB",
  gene = "Vgene",
  group.by = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR, combineBCR, or combineExpression.
chain	"TRA", "TRB", "TRG", "TRG", "IGH", "IGL".
gene	"V", "D" or "J".
group.by	The variable to use for grouping.
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot of percentage of indicated genes as a heatmap

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
percentGenes(combined, 
             chain = "TRB", 
             gene = "Vgene")

ncborcherding/scRepertoire documentation built on April 27, 2024, 8:34 p.m.