plotTrackSingular: Highlight clones

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

Highlight clones

Description

Create alluvial plots highlighting each sequence in amino acid list

Usage

plotTrackSingular(clone_table)

highlightPlot(aseq, clone_table)

Arguments

clone_table	tibble of productive amino acid sequences to highlight generated by LymphoSeq function cloneTrack
aseq	CDR3 amino acid sequence to highlight

Details

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

Value

A list of alluvial plots highlighting a single sequence

Functions

• highlightPlot(): Highlight a specific amino acid sequence

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")
top_seq <- LymphoSeq2::topSeqs(amino_table, top = 3)
clone_table <- LymphoSeq2::cloneTrack(
  study_table = top_seq,
  sample_list = c("TRB_CD8_949", "TRB_CD8_CMV_369")
)
LymphoSeq2::plotTrackSingular(clone_table)

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