plotTrack: Clone tracking alluvial plot

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Clone tracking alluvial plot

Description

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

Details

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

Value

An alluvial diagram tracking particular clone across samples.

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)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.