VDJ_logoplot_vector

Plots a logoplot of the CDR3 aminoacid region

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_logoplot_vector function

<dl><dt>cdr3.vector</dt>
<dd>A character vector of aa sequences. This is to increase flexibility of this function. Such a sequence vector may be retrieved from the VDJ_analyse function output on a clonotype level or from the VDJ_GEX_matrix function output on a per cell level. Additionally, any length of sequence may be used (e.g. HCDR3 only or H and LCDR3 pasted together)</dd>
<dt>length_cdr3</dt>
<dd>Integer or character. Defaults to "auto". Sets the length of the CDR3 regions that are selected to be plotted. If set to auto, the most frequently appearing length in the vector will be used</dd>
<dt>seq_type</dt>
<dd>passed to ggseqlogo. Can be set to "aa", "dna", "rna" or "other"</dd>
<dt>namespace</dt>
<dd>passed to ggseqlogo. Default "auto".</dd>
<dt>font</dt>
<dd>passed to ggseqlogo. Default "roboto_medium".</dd>
<dt>method</dt>
<dd>passed to ggseqlogo. Default "bits".</dd></dl>

Arguments

Flexible logoplot wrapper — VDJ_logoplot_vector

<dl>

<dt>cdr3.vector</dt>
<dd>A character vector of aa sequences. This is to increase flexibility of this function. Such a sequence vector may be retrieved from the VDJ_analyse function output on a clonotype level or from the VDJ_GEX_matrix function output on a per cell level. Additionally, any length of sequence may be used (e.g. HCDR3 only or H and LCDR3 pasted together)</dd>


<dt>length_cdr3</dt>
<dd>Integer or character. Defaults to "auto". Sets the length of the CDR3 regions that are selected to be plotted. If set to auto, the most frequently appearing length in the vector will be used</dd>


<dt>seq_type</dt>
<dd>passed to ggseqlogo. Can be set to "aa", "dna", "rna" or "other"</dd>


<dt>namespace</dt>
<dd>passed to ggseqlogo. Default "auto".</dd>


<dt>font</dt>
<dd>passed to ggseqlogo. Default "roboto_medium".</dd>


<dt>method</dt>
<dd>passed to ggseqlogo. Default "bits".</dd>

</dl>

Flexible logoplot wrapper

VDJ_logoplot_vector: Flexible logoplot wrapper

Description

Usage

Value

Arguments

Examples