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Plot rarefaction and extrapolation curves for samples

Source: R/rarefactionCurve.R
plotRarefactionCurve.Rd

Given a study table, for each sample plot rarefaction curves to estimate repertoire diversity. The method used to generate the rarefaction curve is derived from Chao et al., (2014) using the iNEXT library

Usage

plotRarefactionCurve(study_table, endpoint = 1e+05)

Arguments

study_table

A tibble consisting antigen receptor sequencing data imported by the LymphoSeq2 function readImmunoSeq(). "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns.

endpoint

An integer specifying the endpoint for rarefaction and extrapolation. Default is 100000.

See also

runINext()

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
#> Dataset Analysis:
#>   Files: 10, Total: 0.00 GB, Largest: 0.0 MB
#>   Available memory: 12.0 GB
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
LymphoSeq2::plotRarefactionCurve(study_table)