chordDiagramVDJ: Chord diagram of VJ or DJ gene associations

In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Creates a chord diagram showing VJ or DJ gene associations from one or more samples.

Usage

chordDiagramVDJ(sample, association = "VJ", colors = c("red", "blue"))

Arguments

sample	A data frame consisting of frequencies of antigen receptor sequences. "vFamilyName", "jFamilyName", and if applicable, "dFamilyName" are a required columns. Using output from the LymphoSeq function topSeqs is recommended.
association	A character vector of gene familes to associate. Options include "VJ" or "DJ".
colors	A character vector of 2 colors corresponding to the V/D and J gene colors respectively.

Details

The size of the ribbons connecting VJ or DJ genes correspond to the number of samples or number of sequences that make up that recombination event. The thicker the ribbon, the higher the frequency of the recombination.

Value

Returns a chord diagram showing VJ or DJ gene associations from one or more samples.

See Also

topSeqs

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.nt <- productiveSeq(file.list = file.list, aggregate = "nucleotide")

top.seqs <- topSeqs(productive.seqs = productive.nt, top = 1)

chordDiagramVDJ(sample = top.seqs, association = "VJ", colors = c("red", "blue"))

# Remove "TCRB" from gene family name
top.seqs <- as.data.frame(apply(top.seqs, 2, function(x) gsub("TCRB", "", x)))

chordDiagramVDJ(sample = top.seqs, association = "VJ", colors = c("red", "blue"))

Example output

Loading required package: LymphoSeqDB
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.

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LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.