percentVJ: Quantifying the V and J gene usage across clones

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

Quantifying the V and J gene usage across clones

Description

This function the proportion V and J genes used by grouping variables for an indicated chain to produce a matrix of VJ gene pairings.

Usage

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

Arguments

input.data	The product of combineTCR, combineBCR, or combineExpression.
chain	"TRA", "TRB", "TRG", "TRG", "IGH", "IGL"
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 V and J gene pairings as a heatmap

Examples

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

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