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Last data update: 2014.03.03

R: Chord diagram of VJ or DJ gene associations

chordDiagramVDJ

R Documentation

Chord diagram of VJ or DJ gene associations

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.

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"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/chordDiagramVDJ.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chordDiagramVDJ
> ### Title: Chord diagram of VJ or DJ gene associations
> ### Aliases: chordDiagramVDJ
> 
> ### ** Examples
> 
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
> 
> file.list <- readImmunoSeq(path = file.path)
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> productive.nt <- productiveSeq(file.list = file.list, aggregate = "nucleotide")
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> 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"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>