HaplotypeVisualizer

A web-based visualization tool for polyploid haplotypes.

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Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • CLI
   • Run
3. Usage
4. License
5. Contact
6. Acknowledgments

About The Project

HaplotypeVisualizer is a graph-based web-app for polyploid haplotype visualization. It interactively visualizes the differences between haplotypes and includes features such as bookmarking, pre-processing and phenotype meta-data support.

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Built With

• React.js
• Cytoscape.js
• FastAPI

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Getting Started

Tip

It is recommended to use a virtual environment manager such as Conda or venv to avoid package versioning problems.

Important:

Make sure to have pip and nodejs installed on your machine!

Start by cloning this repository to your machine. E.g., like so:

git clone https://github.com/ethan-keller/HaplotypeVisualizer

For other ways to clone a repository to your machine: GitHub Cloning Docs

CLI

To get HaplotypeVisualizer up and running, you need to install the haplovis CLI (Command Line Interface).

1. Open a terminal in the root directory: /HaplotypeVisualizer

2. Install the haplovis package and its dependencies:

   pip install .

3. To verify that the installation was successfull, try to use the haplovis CLI:

   haplovis --help

Run

This section explains how you can build and start the HaplotypeVisualizer web-app.

1. Build HaplotypeVisualizer (installs dependencies + builds a production react app)

   haplovis build

2. Start HaplotypeVisualizer (starts a static server and a backend server)

   haplovis start

   or specify an optional port (--port / -p) and/or your data folder:

   haplovis start -p 9999 -f ./my-data-folder

   Important:

   • Default port: 3000
   • Default data folder: /data

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Usage

In the import table on the welcome view, you must import files that are located in your previously specified data folder (as explained in the Run section). If you did not specify a folder, the default one will be used which is the HaplotypeVisualizer/data directory. Move your files to this folder or use one of the provided data files (already located in this directory).

Below is a table of the given demo GFA files with their respective phenotype tables:

GFA file	Phenotable
15GFA.gfa	15GFA_phenos.csv
50bubbles6paths.gfa	50bubbles6paths_phenos.csv
demo1.gfa	demo1.csv
demo2.gfa	demo2.csv
2kbubbles.gfa	NA
5kbubbles.gfa	NA
10kbubbles.gfa	NA
L3000N4P.gfa	NA
L100N10P.gfa	NA

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License

BSD 3-clause

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Contact

Ethan Keller - e.keller@student.tudelft.nl

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Acknowledgments

I'd like to thank Dr. Thomas Abeel, Lucas van Dijk and the AbeelLab team for guiding and assisting me throughout this project. Additionally, Colin Diesh and Bandage were a great source of inspiration.

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