Highlight clones

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

Value

A list of alluvial plots highlighting a single sequence

Details

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

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)
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