Package: jellyfisher 1.0.4
Kari Lavikka
jellyfisher: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
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>).
Authors:
jellyfisher_1.0.4.tar.gz
jellyfisher_1.0.4.tar.gz(r-4.5-noble)jellyfisher_1.0.4.tar.gz(r-4.4-noble)
jellyfisher_1.0.4.tgz(r-4.4-emscripten)jellyfisher_1.0.4.tgz(r-4.3-emscripten)
jellyfisher.pdf |jellyfisher.html✨
jellyfisher/json (API)
NEWS
| # Install 'jellyfisher' in R: |
| install.packages('jellyfisher', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hautaniemilab/jellyfisher/issues
Pkgdown site:https://hautaniemilab.github.io
- jellyfisher_example_tables - Jellyfisher example data
visualizationphylogeneticssoftwarespatial
Last updated 1 months agofrom:ba102e8682. Checks:2 OK, 1 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 08 2025 |
| R-4.5-linux | OK | Mar 08 2025 |
| R-4.4-linux | NOTE | Mar 08 2025 |
Exports:extract_tables_from_clonevoljellyfisherjellyfisherOutputrenderJellyfisherselect_patientsset_parentsset_ranks
Dependencies:base64encbslibcachemclidigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigR6rappdirsrlangrmarkdownsassstringistringrtibbletidyselecttinytexutf8vctrswithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract Data for Jellyfisher from ClonEvol Results | extract_tables_from_clonevol |
| Creates a Jellyfish plot | jellyfisher |
| Jellyfisher example data | jellyfisher_example_tables |
| Shiny bindings for jellyfisher | jellyfisher-shiny jellyfisherOutput renderJellyfisher |
| Filter Jellyfish tables by patient | select_patients |
| Set parents for samples | set_parents |
| Set ranks for samples | set_ranks |
| Validate Jellyfish tables | validate_tables |
