{"id":20387038,"url":"https://github.com/cmdcolin/jbrowse_piechart","last_synced_at":"2025-04-12T10:07:05.937Z","repository":{"id":42950333,"uuid":"233141215","full_name":"cmdcolin/jbrowse_piechart","owner":"cmdcolin","description":"A jbrowse plugin that plots the variant data as a piechart","archived":false,"fork":false,"pushed_at":"2023-09-10T01:41:34.000Z","size":751,"stargazers_count":4,"open_issues_count":6,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-12T10:05:08.944Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-01-10T22:31:47.000Z","updated_at":"2023-04-14T07:16:12.000Z","dependencies_parsed_at":"2022-09-22T05:04:57.943Z","dependency_job_id":"28028af3-5d35-48b1-8e0d-efaa4d403154","html_url":"https://github.com/cmdcolin/jbrowse_piechart","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse_piechart","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse_piechart/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse_piechart/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse_piechart/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/jbrowse_piechart/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248550634,"owners_count":21122933,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-15T02:42:24.137Z","updated_at":"2025-04-12T10:07:05.917Z","avatar_url":"https://github.com/cmdcolin.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# piechart_plugin\n\nA JBrowse plugin for plotting allele frequencies as a track glyph\n\n\n## Screenshot\n\n![](img/t11.png)\n\nShowing 1000 genomes pseudo data variant and non-variant frequencies\n\n\n## Example config\n\n\n### Pie glyph (calculates from hom/het from genotypes)\n\nThis shows allele frequencies calculated from multi-sample VCF\n\n    {\n        \"label\": \"Allele frequencies\",\n        \"urlTemplate\": \"file.test.vcf.gz\",\n        \"glyph\": \"PiechartPlugin/View/FeatureGlyph/Pie\",\n        \"style\": {\n            \"variantColor\": \"brown\",\n            \"nonvariantColor\": \"purple\"\n        }\n    }\n\nIn tracks.conf format\n\n    [tracks.allele_freq]\n    key=Allele frequencies\n    urlTemplate=volvox.test.vcf.gz\n    glyph=PiechartPlugin/View/FeatureGlyph/Pie\n\n\n### PieAF glyph (calculates from the AF INFO tag)\n\nThis shows allele-frequency calculated from just using the AF tag in the info field\n\n    [tracks.allele_freq]\n    key=Allele frequencies\n    urlTemplate=volvox.test.vcf.gz\n    glyph=PiechartPlugin/View/FeatureGlyph/PieAF\n    style.variantColor=grey,pink,brown\n\nThe style.variantColor is optional, a default set of grey,blue,red,green\n\n\n## Configuration\n\n\n- glyph - can be PiechartPlugin/View/FeatureGlyph/PieAF or PiechartPlugin/View/FeatureGlyph/Pie\n- style.height - changes diameter of the drawn circle\n- style.variantColor - with PieAF glyph, this is a comma separated list. With Pie glyph it is the color for any alt allele: default green\n- style.nonvariantColor - the Pie glyph this is the color for the ref allele: default orange\n\n## Test data\n\nSee test/data/ folder for example\n\nVisit http://localhost/jbrowse/?data=plugins/PiechartPlugin/test/data to verify your installation\n\n## Installation\n\nClone the repository to the jbrowse plugins subdirectory and name it PiechartPlugin\n\n    git clone https://github.com/cmdcolin/jbrowse_piechart PiechartPlugin\n\nThen add the plugin to your configuration, e.g. \"plugins\": [\"PiechartPlugin\"]\n\nSee http://gmod.org/wiki/JBrowse_FAQ#How_do_I_install_a_plugin for details\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse_piechart","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fjbrowse_piechart","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse_piechart/lists"}