Quantifying the V and J gene usage across clones

Source: R/percentVJ.R

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

percentVJ(
  input.data,
  chain = "TRB",
  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"

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 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")