plot_mut_history

A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Teng Gao

numbat

Haplotype-Aware CNV Analysis from scRNA-Seq

Ruslan Soldatov

Hirak Sarkar

Evan Biederstedt

Peter Kharchenko

plot_mut_history function

<dl><dt>G</dt>
<dd>igraph Mutation history graph</dd>
<dt>clone_post</dt>
<dd>dataframe Clone assignment posteriors</dd>
<dt>edge_label_size</dt>
<dd>numeric Size of edge label</dd>
<dt>node_label_size</dt>
<dd>numeric Size of node label</dd>
<dt>node_size</dt>
<dd>numeric Size of nodes</dd>
<dt>arrow_size</dt>
<dd>numeric Size of arrows</dd>
<dt>show_clone_size</dt>
<dd>logical Whether to show clone size</dd>
<dt>show_distance</dt>
<dd>logical Whether to show evolutionary distance between clones</dd>
<dt>legend</dt>
<dd>logical Whether to show legend</dd>
<dt>edge_label</dt>
<dd>logical Whether to label edges</dd>
<dt>node_label</dt>
<dd>logical Whether to label nodes</dd>
<dt>horizontal</dt>
<dd>logical Whether to use horizontal layout</dd>
<dt>pal</dt>
<dd>named vector Node colors</dd></dl>

Arguments

Plot mutational history — plot_mut_history

<dl>

<dt>G</dt>
<dd>igraph Mutation history graph</dd>


<dt>clone_post</dt>
<dd>dataframe Clone assignment posteriors</dd>


<dt>edge_label_size</dt>
<dd>numeric Size of edge label</dd>


<dt>node_label_size</dt>
<dd>numeric Size of node label</dd>


<dt>node_size</dt>
<dd>numeric Size of nodes</dd>


<dt>arrow_size</dt>
<dd>numeric Size of arrows</dd>


<dt>show_clone_size</dt>
<dd>logical Whether to show clone size</dd>


<dt>show_distance</dt>
<dd>logical Whether to show evolutionary distance between clones</dd>


<dt>legend</dt>
<dd>logical Whether to show legend</dd>


<dt>edge_label</dt>
<dd>logical Whether to label edges</dd>


<dt>node_label</dt>
<dd>logical Whether to label nodes</dd>


<dt>horizontal</dt>
<dd>logical Whether to use horizontal layout</dd>


<dt>pal</dt>
<dd>named vector Node colors</dd>

</dl>

Plot mutational history

plot_mut_history: Plot mutational history

Description

Usage

Value

Arguments

Examples