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piechart_plugin

A JBrowse plugin for plotting allele frequencies as a track glyph

Screenshot

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