VDJ_Vgene_usage

Produces a matrix counting the number of occurences for each VDJ and VJ Vgene combinations for each list enty in VDJ.clonotype.output or for each sample_id in VDJ.matrix

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Alexander Yermanos

Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis

Andreas Agrafiotis

Victor Kreiner

Tudor-Stefan Cotet

Raphael Kuhn

Danielle Shlesinger

Jiami Han

Vittoria Martinolli D'Arcy

Lucas Stalder

Daphne van Ginneken

VDJ_Vgene_usage function

<dl><dt>VDJ</dt>
<dd>For platypus.version = "v2" output from VDJ_analyze function. This should be a list of clonotype dataframes, with each list element corresponding to a single VDJ repertoire. For platypus.version = "v3" output VDJ dataframe from VDJ_GEX_matrix function (VDJ_GEX_matrix.output[[1]])</dd>
<dt>group.by</dt>
<dd>Character. Defaults to "sample_id". Column name of VDJ to group plot by.</dd>
<dt>platypus.version</dt>
<dd>Character. Defaults to "v3". Can be "v2" or "v3" dependent on the input format</dd></dl>

Arguments

V(D)J gene usage stacked barplots — VDJ_Vgene_usage

<dl>

<dt>VDJ</dt>
<dd>For platypus.version = "v2" output from VDJ_analyze function. This should be a list of clonotype dataframes, with each list element corresponding to a single VDJ repertoire. For platypus.version = "v3" output VDJ dataframe from VDJ_GEX_matrix function (VDJ_GEX_matrix.output[[1]])</dd>


<dt>group.by</dt>
<dd>Character. Defaults to "sample_id". Column name of VDJ to group plot by.</dd>


<dt>platypus.version</dt>
<dd>Character. Defaults to "v3". Can be "v2" or "v3" dependent on the input format</dd>

</dl>

V(D)J gene usage stacked barplots

VDJ_Vgene_usage: V(D)J gene usage stacked barplots

Description

Usage

Value

Arguments

Examples