clonalRarefaction: Calculate rarefaction based on the abundance of clones

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

Calculate rarefaction based on the abundance of clones

Description

This functions uses the Hill numbers of order q: species richness (q = 0), Shannon diversity (q = 1), the exponential of Shannon entropy and Simpson diversity (q = 2, the inverse of Simpson concentration) to compute diversity estimates for rarefaction and extrapolation. The function relies on the iNEXT R package. Please read and cite the manuscript if using this function. The input into the iNEXT calculation is abundance, incidence-based calculations are not supported.

Usage

clonalRarefaction(
  input.data,
  cloneCall = "strict",
  chain = "both",
  group.by = NULL,
  plot.type = 1,
  hill.numbers = 0,
  n.boots = 20,
  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".
group.by	The variable to use for grouping.
plot.type	sample-size-based rarefaction/extrapolation curve (type = 1); sample completeness curve (type = 2); coverage-based rarefaction/extrapolation curve (type = 3).
hill.numbers	The Hill numbers to be plotted out (0 - species richness, 1 - Shannon, 2 - Simpson)
n.boots	The number of bootstraps to downsample in o rder to get mean diversity.
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.

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
clonalRarefaction(combined[c(1,2)], cloneCall = "gene", n.boots = 3)

ncborcherding/scRepertoire documentation built on April 7, 2024, 12:44 a.m.