Calculate rarefaction based on the abundance of clones

Source: R/clonalRarefaction.R

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::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.

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

Defines the clonal sequence grouping. Accepted values are: gene (VDJC genes), nt (CDR3 nucleotide sequence), aa (CDR3 amino acid sequence), or strict (VDJC + nt). A custom column header can also be used.

chain

The TCR/BCR chain to use. Use both to include both chains (e.g., TRA/TRB). Accepted values: TRA, TRB, TRG, TRD, IGH, IGL (for both light chains), both.

group.by

A column header in the metadata or lists to group the analysis by (e.g., "sample", "treatment"). If NULL, data will be analyzed by list element or active identity in the case of single-cell objects.

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 bootstrap replicates used to derive confidence intervals for the diversity estimates. More replicates can provide a more reliable measure of statistical variability.

exportTable

If TRUE, returns a data frame or matrix of the results instead of a plot.

palette

Colors to use in visualization - input any hcl.pals.

...

Additional arguments passed to the ggplot theme

Examples

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