combined_pbmc

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=APackOfTheClones&version=1.2.1" alt="[Stable]"></a>
Generated with <code>scRepertoire::combineExpression</code>. To construct this object
from scratch, try:
scRepertoire::combineExpression(scRepertoire::combineTCR(get(data("contig_list", , package = "scRepertoire")), samples = c("P17B", "P17L", "P18B", , "P18L", "P19B", "P19L", "P20B", "P20L"), removeNA = FALSE, , removeMulti = FALSE, filterMulti = FALSE), get(data("scRep_example", , package = "scRepertoire")), cloneCall = "gene", proportion = TRUE)

datasets

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Qile Yang

APackOfTheClones

Visualization of Clonal Expansion for Single Cell Immune
Profiles

combined_pbmc function

A Seurat object with the following slots filled<dl>
<dt>assays</dt>
<dd>
<ul>
<li>counts - Raw expression data</li>
<li>data - Normalized expression data</li>
<li>scale.data - Scaled expression data</li>
<li>var.features - names of the current features selected as variable</li>
<li>meta.features - Assay level metadata such as mean and variance</li>
</ul></dd><dt>meta.data</dt>
<dd>Cell level metadata with a combined TCR contig list <code>from scRepertoire</code></dd><dt>active.assay</dt>
<dd>Current default assay</dd><dt>active.ident</dt>
<dd>Current default idents</dd><dt>graphs</dt>
<dd>Neighbor graphs computed, currently stores the SNN</dd><dt>reductions</dt>
<dd>Dimensional reductions: UMAP</dd><dt>version</dt>
<dd>Seurat version used to create the object</dd><dt>commands</dt>
<dd>Command history, including the one used to create this object "combineExpression"</dd>
</dl>

Format

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Generated with <code>scRepertoire::combineExpression</code>. To construct this object
from scratch, try:
scRepertoire::combineExpression(scRepertoire::combineTCR(get(data("contig_list", , package = "scRepertoire")), samples = c("P17B", "P17L", "P18B", , "P18L", "P19B", "P19L", "P20B", "P20L"), removeNA = FALSE, , removeMulti = FALSE, filterMulti = FALSE), get(data("scRep_example", , package = "scRepertoire")), cloneCall = "gene", proportion = TRUE)

Example Multi-sampled T-cell seurat object with integrated TCR library — combined_pbmc

A Seurat object with the following slots filled<dl>
<dt>assays</dt>
<dd>
<ul>
<li>counts - Raw expression data</li>
<li>data - Normalized expression data</li>
<li>scale.data - Scaled expression data</li>
<li>var.features - names of the current features selected as variable</li>
<li>meta.features - Assay level metadata such as mean and variance</li>
</ul></dd>

<dt>meta.data</dt>
<dd>Cell level metadata with a combined TCR contig list <code>from scRepertoire</code></dd>

<dt>active.assay</dt>
<dd>Current default assay</dd>

<dt>active.ident</dt>
<dd>Current default idents</dd>

<dt>graphs</dt>
<dd>Neighbor graphs computed, currently stores the SNN</dd>

<dt>reductions</dt>
<dd>Dimensional reductions: UMAP</dd>

<dt>version</dt>
<dd>Seurat version used to create the object</dd>

<dt>commands</dt>
<dd>Command history, including the one used to create this object "combineExpression"</dd>


</dl>

combined_pbmc: Example Multi-sampled T-cell seurat object with integrated TCR library

Description

Usage

Arguments

Format