plotClusterComparison

Creates a comparison visualization showing cluster assignments from both methods.

Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires.
The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes.
The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.

Ayelet Peres

piglet

Program for Inferring Immunoglobulin Allele Similarity Clusters
and Genotypes

William Lees

Gur Yaari

plotClusterComparison function

<dl><dt>hierarchical_result</dt>
<dd>GermlineCluster object from hierarchical clustering</dd>
<dt>leiden_result</dt>
<dd>GermlineCluster object from Leiden clustering</dd>
<dt>...</dt>
<dd>Additional arguments</dd></dl>

Arguments

Compare hierarchical and Leiden clustering — plotClusterComparison

<dl>

<dt>hierarchical_result</dt>
<dd>GermlineCluster object from hierarchical clustering</dd>


<dt>leiden_result</dt>
<dd>GermlineCluster object from Leiden clustering</dd>


<dt>...</dt>
<dd>Additional arguments</dd>

</dl>

plotClusterComparison: Compare hierarchical and Leiden clustering

Description

Usage

Value

Arguments

See Also