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 percentVJ().

Usage

percentGenes(
  input.data,
  chain = "TRB",
  gene = "Vgene",
  group.by = NULL,
  order.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
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order
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 Nov. 5, 2024, 2:05 p.m.