motif_plot_large

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).

Enhancing T cell receptor (TCR) sequence analysis, 'ClusTCR2', based on 'ClusTCR' python program, leverages Hamming distance to compare the complement-determining region three (CDR3) sequences for sequence similarity, variable gene (V gene) and length. The second step employs the Markov Cluster Algorithm to identify clusters within an undirected graph, providing a summary of amino acid motifs and matrix for generating network plots. Tailored for single-cell RNA-seq data with integrated TCR-seq information, 'ClusTCR2' is integrated into the Single Cell TCR and Expression Grouped Ontologies (STEGO) R application or 'STEGO.R'. See the two publications for more details. Sebastiaan Valkiers, Max Van Houcke, Kris Laukens, Pieter Meysman (2021) <doi:10.1093/bioinformatics/btab446>, Kerry A. Mullan, My Ha, Sebastiaan Valkiers, Nicky de Vrij, Benson Ogunjimi, Kris Laukens, Pieter Meysman (2023) <doi:10.1101/2023.09.27.559702>.

Kerry A. Mullan

ClusTCR2

Identifying Similar T Cell Receptor Hyper-Variable Sequences
with 'ClusTCR2'

Sebastiaan Valkiers

Kris Laukens

Pieter Meysman

motif_plot_large function

<dl><dt>ClusTCRFile_large</dt>
<dd>Matrix file produced from mcl_cluster_large.</dd>
<dt>Clust_column_name</dt>
<dd>Name of clustering column from mcl_cluster file e.g. cluster.</dd>
<dt>Clust_selected</dt>
<dd>Select which cluster to display. Only one at a time.</dd></dl>

Arguments

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details). — motif_plot_large

<dl>

<dt>ClusTCRFile_large</dt>
<dd>Matrix file produced from mcl_cluster_large.</dd>


<dt>Clust_column_name</dt>
<dd>Name of clustering column from mcl_cluster file e.g. cluster.</dd>


<dt>Clust_selected</dt>
<dd>Select which cluster to display. Only one at a time.</dd>

</dl>

motif_plot_large: Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).

Description

Usage

Value

Arguments