set_ranks

Given a list of jellyfish input tables and a named list of ranks for each
sample, set the rank for each sample.

Generates interactive Jellyfish plots to visualize spatiotemporal tumor
evolution by integrating sample and phylogenetic trees into a unified plot.
This approach provides an intuitive way to analyze tumor heterogeneity and
evolution over time and across anatomical locations. The Jellyfish plot
visualization design was first introduced by Lahtinen, Lavikka, et al.
(2023, <doi:10.1016/j.ccell.2023.04.017>).
This package also supports visualizing ClonEvol results, a tool developed
by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal
evolution from multi-sample sequencing data. The 'clonevol' package is not
available on CRAN but can be installed from its GitHub
repository (<https://github.com/hdng/clonevol>).

Kari Lavikka

jellyfisher

Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots

set_ranks function

<dl><dt>tables</dt>
<dd>A list of tables (samples, phylogeny, compositions, ranks)</dd>
<dt>ranks</dt>
<dd>A named list of ranks for each sample</dd>
<dt>default</dt>
<dd>The default rank to use when a sample is not in the rank list
(default: 1)</dd></dl>

Arguments

Set ranks for samples — set_ranks

<dl>

<dt>tables</dt>
<dd>A list of tables (samples, phylogeny, compositions, ranks)</dd>


<dt>ranks</dt>
<dd>A named list of ranks for each sample</dd>


<dt>default</dt>
<dd>The default rank to use when a sample is not in the rank list
(default: 1)</dd>

</dl>

set_ranks: Set ranks for samples

Description

Usage

Value

Arguments

Examples