clonalQuant: Quantify the unique clones by group or sample

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

Quantify the unique clones by group or sample

Description

This function quantifies unique clones. The unique clones can be either reported as a raw output or scaled to the total number of clones recovered using the scale parameter.

Usage

clonalQuant(
  input.data,
  cloneCall = "strict",
  chain = "both",
  scale = FALSE,
  group.by = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR, combineBCR, or combineExpression.
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"
scale	Converts the graphs into percentage of unique clones.
group.by	The column header used 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 the total or relative unique clones

Examples

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

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