Quantify the unique clones by group or sample

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.

clonalQuant(
  input.data,
  cloneCall = "strict",
  chain = "both",
  scale = FALSE,
  group.by = NULL,
  order.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

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 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)