From 102b41d0561e147d69186901c8f8563cbcc41f7d Mon Sep 17 00:00:00 2001 From: Kari Lavikka Date: Thu, 3 Oct 2024 16:11:54 +0300 Subject: [PATCH] update README --- README.md | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 4edae5c..d6b0ad1 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,11 @@ -# Jellyfish – A Tumor Evolution Visualization Tool +# Jellyfish: A Tumor Evolution Visualization Tool Jellyfish automates the creation of Jellyfish plots based on the output from [ClonEvol](https://doi.org/10.1093/annonc/mdx517) or similar tools that infer -tumor phylogeny and subclonal composition. The Jellyfish visualization design -was first introduced in the following paper: +tumor phylogeny and subclonal composition. These plots integrate a hierarchical +sample structure and tumor phylogeny into a single visualization, allowing for +the display of both spatial and temporal evolution of the tumor. The design of +the Jellyfish plot was first introduced in the following paper: Lahtinen, A., Lavikka, K., Virtanen, A., et al. "Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian @@ -25,7 +27,7 @@ The documentation is still somewhat incomplete. Stay tuned! ## Basic Concepts Jellyfish plots visualize the evolution of a tumor by showing the subclonal -composition of samples in a phylogenetic context. The plot combined two trees +composition of samples in a phylogenetic context. The plot combines two trees into a single visualization: a **phylogeny** and a **sample tree**. The **phylogeny** is a tree structure that represents the evolutionary @@ -61,13 +63,18 @@ subclones that have been observed in multiple real samples. - Visualizes tumor phylogeny and subclonal compositions as a Jellyfish plot. - Allows visualizing both temporal and spatial relationships between samples. - Sorts samples based on the subclonal composition and divergence, effectively grouping similar samples together. -- Provides basic interactivity for exploring the plot: highlighting subclones and cluster across the plot upon hover or clicking, displays details in tooltips. +- Provides basic interactivity for exploring the plot, such as highlighting subclones and clusters upon hover or click, and displaying details in tooltips. - Generates phylogeny-aware color schemes for subclones, inspired by [Visualizing Clonal Evolution in Cancer](http://dx.doi.org/10.1016/j.molcel.2016.05.025) by Krzywinski. - Exports the plot as publication-ready SVG or PNG files. - Adjustable layout parameters for fine-tuning the plot appearance. ## Getting Started +If you are an R user, you may want to use the +[Jellyfisher](https://github.com/HautaniemiLab/jellyfisher) R package to +generate Jellyfish plots in RStudio, R Markdown, Shiny apps, or plain R. +Otherwise, continue reading. + Jellyfish is a web application written in TypeScript. You need to have [Node.js](https://nodejs.org/) installed to run the tool. @@ -78,8 +85,8 @@ Jellyfish is a web application written in TypeScript. You need to have 4. `npm run dev` (starts a development server) Once the development server is running, open your browser and navigate to -http://localhost:5173/. You should see the Jellyfish Plotter interface, which -allows you to render Jellyfish plots based on your data. +http://localhost:5173/. You should see the user interface, which allows you to +render Jellyfish plots based on your data. ## Input Data @@ -202,9 +209,9 @@ TODO: Docs ## About -Copyright (c) 2024 Kari Lavikka. See [LICENSE](LICENSE) for details. +Copyright (c) 2024 Kari Lavikka. MIT licensed, see [LICENSE](LICENSE) for details. -Jellyfish Plotter is developed in [The Systems Biology of Drug Resistance in +Jellyfish is developed in [The Systems Biology of Drug Resistance in Cancer](https://www.helsinki.fi/en/researchgroups/systems-biology-of-drug-resistance-in-cancer) group at the [University of Helsinki](https://www.helsinki.fi/en).