Science Score: 57.0%
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords
Repository
R htmlwidget for Jellyfish
Basic Info
- Host: GitHub
- Owner: HautaniemiLab
- License: other
- Language: R
- Default Branch: main
- Homepage: https://hautaniemilab.github.io/jellyfisher/
- Size: 2.45 MB
Statistics
- Stars: 6
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 4
Topics
Metadata Files
README.md
Jellyfisher
Jellyfisher is an R package for visualizing tumor evolution and subclonal compositions using Jellyfish plots, which display both spatial and temporal dimensions in a single unified figure.
The package is based on the Jellyfish visualization tool, bringing its functionality to R users. Jellyfisher supports both ClonEvol results and plain data frames, making it compatible with various tools and workflows.
Installation
Install from CRAN
R
install.packages("jellyfisher")
Or alternatively, install the latest development version from GitHub
R
devtools::install_github("HautaniemiLab/jellyfisher", build_vignettes = TRUE)
Usage
Jellyfisher is designed to work with data frames or ClonEvol results.
Plotting Data Frames
The input data should follow specific structures for samples, phylogeny, and
subclonal compositions, which are described in the
jellyfisher
function's documentation.
Example
```R library(jellyfisher)
Plot the bundled example data
jellyfisher(jellyfisherexampletables) ```
Plotting ClonEvol Results
Jellyfisher provides a straightforward way to visualize
ClonEvol results using the
extract_tables_from_clonevol
function. See the reference page for details.
Example
```R library(clonevol) library(jellyfisher)
Run ClonEvol. Check the ClonEvol documentation for details.
y <- infer.clonal.models(...) y <- convert.consensus.tree.clone.to.branch(y)
Plot the results
extracttablesfrom_clonevol(y, model = 1) |> jellyfisher() ```
Setting Parent-Child Relationships of Samples
By default, all samples that have no explicit parent are children of the
inferred root sample. You can customize the parent-child relationships by
modifying the parent column in the samples data frame before plotting.
You can also modify the relationships with ease using the
set_parents
function.
For example, if you have three samples, A, B, and C, they will have the following relationships by default:
Root
/ | \
A B C
With the explicit parents, you can customize the relationships:
R
tables |>
set_parents(list(
# The parent of C is B
"C" = "B"
) |>
jellyfisher()
Root
/ \
A B
\
C
Contributing
Jellyfisher is a thin wrapper for the
Jellyfish visualization tool.
Jellyfish is included as a git submodule in the
tools/ directory.
To build the Jellyfish JavaScript dependency, run the
update-and-build.sh
script in the
tools/
directory. Most of the R code is autogenerated from the Jellyfish JavaScript
code using the
generate-R-code.mjs
script, which should be run after building the Jellyfish dependency.
Citation
If you use Jellyfisher in your research, please cite the following paper:
Kari Lavikka, Altti Ilari Maarala, Jaana Oikkonen, Sampsa Hautaniemi, Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics, Bioinformatics, 2025;, btaf091, https://doi.org/10.1093/bioinformatics/btaf091
About
Copyright (c) 2025 Kari Lavikka. MIT license, see LICENSE.md for details.
Jellyfisher is developed in The Systems Biology of Drug Resistance in Cancer group at the University of Helsinki.
This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreements No. 965193 (DECIDER) and No. 847912 (RESCUER).
Owner
- Name: Hautaniemi Lab
- Login: HautaniemiLab
- Kind: organization
- Location: Finland
- Website: https://www.helsinki.fi/en/researchgroups/systems-biology-of-drug-resistance-in-cancer
- Twitter: HautaniemiLab
- Repositories: 1
- Profile: https://github.com/HautaniemiLab
The Systems Biology of Drug Resistance in Cancer group, University of Helsinki
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lavikka"
given-names: "Kari"
orcid: "https://orcid.org/0000-0002-4163-4945"
title: "Jellyfisher"
url: "https://github.com/HautaniemiLab/jellyfisher"
preferred-citation:
type: article
authors:
- family-names: "Lavikka"
given-names: "Kari"
orcid: "https://orcid.org/0000-0002-4163-4945"
- family-names: "Maarala"
given-names: "Altti Ilari"
orcid: "https://orcid.org/0000-0001-8851-4265"
- family-names: "Oikkonen"
given-names: "Jaana"
orcid: "https://orcid.org/0000-0002-1063-2736"
- family-names: "Hautaniemi"
given-names: "Sampsa"
orcid: "https://orcid.org/0000-0002-7749-2694"
doi: "10.1093/bioinformatics/btaf091"
journal: "Bioinformatics"
title: "Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics"
year: 2025
GitHub Events
Total
- Create event: 4
- Release event: 3
- Issues event: 6
- Watch event: 3
- Issue comment event: 3
- Push event: 51
Last Year
- Create event: 4
- Release event: 3
- Issues event: 6
- Watch event: 3
- Issue comment event: 3
- Push event: 51
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 0
- Average time to close issues: 16 days
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: 16 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tuner (3)
Pull Request Authors
Top Labels
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Packages
- Total packages: 1
-
Total downloads:
- cran 151 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
cran.r-project.org: jellyfisher
Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
- Homepage: https://github.com/HautaniemiLab/jellyfisher
- Documentation: http://cran.r-project.org/web/packages/jellyfisher/jellyfisher.pdf
- License: MIT + file LICENSE
-
Latest release: 1.0.4
published about 1 year ago