https://github.com/cmdcolin/jbrowse_piechart

A jbrowse plugin that plots the variant data as a piechart
https://github.com/cmdcolin/jbrowse_piechart

Last synced: 4 days ago
JSON representation

A jbrowse plugin that plots the variant data as a piechart

• Host: GitHub
• URL: https://github.com/cmdcolin/jbrowse_piechart
• Owner: cmdcolin
• Created: 2020-01-10T22:31:47.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2023-09-10T01:41:34.000Z (about 1 year ago)
• Last Synced: 2024-04-15T02:14:35.856Z (7 months ago)
• Language: JavaScript
• Size: 733 KB
• Stars: 4
• Watchers: 3
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md

Awesome Lists containing this project

README

        
# piechart_plugin

A JBrowse plugin for plotting allele frequencies as a track glyph

## Screenshot

![](img/t11.png)

Showing 1000 genomes pseudo data variant and non-variant frequencies

## Example config

### Pie glyph (calculates from hom/het from genotypes)

This shows allele frequencies calculated from multi-sample VCF

    {

        "label": "Allele frequencies",

        "urlTemplate": "file.test.vcf.gz",

        "glyph": "PiechartPlugin/View/FeatureGlyph/Pie",

        "style": {

            "variantColor": "brown",

            "nonvariantColor": "purple"

        }

    }

In tracks.conf format

    [tracks.allele_freq]

    key=Allele frequencies

    urlTemplate=volvox.test.vcf.gz

    glyph=PiechartPlugin/View/FeatureGlyph/Pie

### PieAF glyph (calculates from the AF INFO tag)

This shows allele-frequency calculated from just using the AF tag in the info field

    [tracks.allele_freq]

    key=Allele frequencies

    urlTemplate=volvox.test.vcf.gz

    glyph=PiechartPlugin/View/FeatureGlyph/PieAF

    style.variantColor=grey,pink,brown

The style.variantColor is optional, a default set of grey,blue,red,green

## Configuration

- glyph - can be PiechartPlugin/View/FeatureGlyph/PieAF or PiechartPlugin/View/FeatureGlyph/Pie

- style.height - changes diameter of the drawn circle

- style.variantColor - with PieAF glyph, this is a comma separated list. With Pie glyph it is the color for any alt allele: default green

- style.nonvariantColor - the Pie glyph this is the color for the ref allele: default orange

## Test data

See test/data/ folder for example

Visit http://localhost/jbrowse/?data=plugins/PiechartPlugin/test/data to verify your installation

## Installation

Clone the repository to the jbrowse plugins subdirectory and name it PiechartPlugin

    git clone https://github.com/cmdcolin/jbrowse_piechart PiechartPlugin

Then add the plugin to your configuration, e.g. "plugins": ["PiechartPlugin"]

See http://gmod.org/wiki/JBrowse_FAQ#How_do_I_install_a_plugin for details