Clone tracking alluvial plot

Creates alluvial tracking amino acid frequencies across multiple samples

Usage

plotTrack(
  clone_table,
  alist = NULL,
  apal = NULL,
  breaks = 2,
  alphas = 0,
  breaks_pal = c("#7fc97f", "#beaed4")
)

Arguments

clone_table

A tibble of productive amino acid sequences generated by LymphoSeq2 function cloneTrack()

alist

An optional list of amino acid, if a list is provided only those sequences will be highlighted

apal

An optional list of palette colors used for the amino acids to be highlighted

breaks

Add an additional band behind the alluvial plot to highlight group, specifies after which bar the break should appear

alphas

Set alpha for the band

breaks_pal

Specify palette for the bands

Value

An alluvial diagram tracking particular clone across samples.

Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1) 
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(study_table,
  aggregate = "junction_aa"
)
clone_table <- LymphoSeq2::cloneTrack(
  study_table = amino_table,
  sample_list = c(
    "TRB_CD8_949",
    "TRB_CD8_CMV_369"
  )
)
LymphoSeq2::plotTrack(clone_table)