Examining the clonal space occupied by specific clones

Source: R/clonalProportion.R

This function calculates the relative clonal space occupied by the clones. The grouping of these clones is based on the parameter clonalSplit, at default, clonalSplit will group the clones into bins of 1:10, 11:100, 101:1001, etc. To adjust the clones selected, change the numbers in the variable split. If a matrix output for the data is preferred, set exportTable = TRUE.

clonalProportion(
  input.data,
  clonalSplit = c(10, 100, 1000, 10000, 30000, 1e+05),
  cloneCall = "strict",
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data

The product of combineTCR(), combineBCR(), or combineExpression().

clonalSplit

The cut points for the specific clones

cloneCall

How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data

chain

indicate if both or a specific chain should be used - e.g. "both", "TRA", "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

Exports a table of the data into the global. environment in addition to the visualization

palette

Colors to use in visualization - input any hcl.pals

Value

ggplot of the space occupied by the specific rank of clones

Examples

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