R/clonalRarefaction.R
clonalRarefaction.Rd
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"
)
The product of combineTCR()
,
combineBCR()
, or combineExpression()
.
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.
indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL".
The variable to use for grouping.
sample-size-based rarefaction/extrapolation curve
(type = 1
); sample completeness curve (type = 2
);
coverage-based rarefaction/extrapolation curve (type = 3
).
The Hill numbers to be plotted out (0 - species richness, 1 - Shannon, 2 - Simpson)
The number of bootstraps to downsample in order to get mean diversity.
Exports a table of the data into the global environment in addition to the visualization.
Colors to use in visualization - input any hcl.pals.
#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)