Demonstrate the relative abundance of clones by group or sample

Displays the number of clones at specific frequencies by sample or group. Visualization can either be a line graph ( scale = FALSE) using calculated numbers or density plot (scale = TRUE). Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.

clonalAbundance(
  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 density plots in order to show relative distributions.
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 to the visualization.
palette: Colors to use in visualization - input any hcl.pals.

Value

ggplot of the total or relative abundance of clones across quanta

Author

Nick Borcherding, Justin Reimertz

Examples

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