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For more information please see:\n\n    http://about.targetvalidation.org\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n    http://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n","_id":"cttv.genome@0.0.29","dist":{"shasum":"46a01769f51ddf7d9144d868cc5fb59afa0b37c3","tarball":"https://registry.npmjs.org/cttv.genome/-/cttv.genome-0.0.29.tgz","integrity":"sha512-yCb8xK+jkgaBOhbL5EMi12sIcgh2p62p1CsVynDTWnjx55j1GAITDfS9oBifMQQg/FiTVEzm/Xe7H91QM5/46g==","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIQCtmWn3UYywfu1Okqd1T6i2s/TwjJmoPJfl3lLhTZPDCAIgc58x7WUTs5P8goloAQskpE36ghBSY6ip/G5xQQw/fs8="}]},"maintainers":[{"name":"emepyc","email":"emepyc@gmail.com"}],"_npmUser":{"name":"emepyc","email":"emepyc@gmail.com"},"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/cttv.genome-0.0.29.tgz_1509724297390_0.7910002088174224"}}},"readme":"\n# CTTV Target Genome Browser\n\nMinimal genome browser built for the CTTV web application.\n\n\n## Installation\n\nFrom Git\n\n````bash\ngit clone https://github.com/CTTV/targetGenomeBrowser\ncd targetGenomeBrowser\nnpm install\nnpm build-browser\n````\n\nFrom npm\n````\nnpm install cttv.genome\n````\n\n## Usage\n\n`cttvGenomeBrowser` is based on [tnt.genome](https://github.com/emepyc/tnt.genome), a library for making minimal genome browsers and displaying genome annotation. Check its documentation for more options.\nExample of usage:\n\n````javascript\n// Define an instance of tnt.genome\nvar gB = tnt.board.genome()\n    .species(\"human\")\n    .gene(\"ENSG00000157764\")\n    .width(950);\n\n// Define and instance of cttv.targetGenomeBrowser\nvar cttvGB = targetGenomeBrowser()\n    .show_snps(false)\n    .show_nav(true);\n\n// Start the genome browser using the tnt.genome in the given div element\ncttvGB (gB, document.getElementById(\"genomeBrowser\"));\n````\nMore examples available in the `examples` folder\n\n## API\n\n`cttvGenomeBrowser` exposes the following methods:\n\n#### show_nav\nIf the buttons-based navigation is included in the display. Defaults to _true_.\n\n````javascript\nvar cttvGB = targetGenomeBrowser()\n    .show_nav(false);\n````\n\n#### show_links\nIf the link to the Ensembl Genome browser in included in the display. Defaults to _true_.\n\n````javascript\nvar cttvGB = targetGenomeBrowser()\n    .show_links(false);\n````\n\n#### show_snps\nIf the SNPs tracks are displayed. Defaults to _true_.\n\n````javascript\nvar cttvGB = targetGenomeBrowser()\n    .show_snps(false);\n````\n\n\n#### track\nReturns a given track by name. The following names are available:\n\n| Name           | Track                                                             |\n| :------------- | :--------------------------------                                 |\n| gene           | The Gene / Transcript track                                       |\n| common_snps    | The track containing SNPs associating the gene to common diseases |\n| rare_snps      | The track containing SNPs associating the gene to reare diseases  |\n\n\n````javascript\nvar cttvGB = targetGenomeBrowser();\nvar geneTrack = cttvGB.track(\"gene\");\n\ngeneTrack.display().on(\"click\", function (gene) {\n    var elem = this;\n    var tooltip_obj = function (g) {\n        var obj = {};\n        obj.header = (g.display_name || g.external_name) + \" (\" + g.id + \")\";\n        obj.rows = [];\n\n        obj.rows.push( {\n            \"label\" : \"Biotype\",\n            \"value\" : g.biotype\n        });\n\n        obj.rows.push( {\n            \"label\" : \"Description\",\n            \"value\" : g.description || g.gene.description\n        });\n\n        return obj;\n    }\n    tnt.tooltip.table()\n        .call(elem, tooltip_obj(gene));\n});\n````\n\nIf any change is made to the _track_ after the plug-in has been initialised (see [tnt.genome](https://github.com/emepyc/tnt.genome) and [tnt.board](https://github.com/emepyc/tnt.board) for examples), the visualisation needs to be re-started using the `start` method\n\n#### start\nRe-start the genome browser after making any change. For example, the following snippet change the gene to be displayed as transcripts when a gene is clicked:\n\n````javascript\ngBTheme(gB, document.getElementById(\"genomeBrowser\"));\n\nvar geneTrack = gBTheme.track(\"gene\");\ngeneTrack.display().on(\"click\", function (gene) {\n    if (!gene.gene) { // It is not a transcript\n        gB.gene (gene.id);\n        gBTheme.start();\n    }\n});\n````\n\n## Feedback\n\nPlease, send any comments, bug reports or features request to support  (_AT_) targetvalidation.org\n","maintainers":[{"name":"emepyc","email":"emepyc@gmail.com"}],"time":{"modified":"2022-06-14T05:34:19.808Z","created":"2016-01-25T16:13:46.855Z","0.0.1":"2016-01-25T16:13:46.855Z","0.0.2":"2016-01-25T16:17:57.875Z","0.0.3":"2016-01-25T16:25:00.970Z","0.0.4":"2016-01-25T16:28:50.505Z","0.0.5":"2016-01-25T16:32:11.504Z","0.0.6":"2016-04-07T13:08:29.598Z","0.0.7":"2016-04-12T01:25:20.244Z","0.0.8":"2016-04-14T23:37:23.721Z","0.0.9":"2016-04-15T11:31:00.567Z","0.0.10":"2016-04-20T16:10:49.186Z","0.0.11":"2016-04-22T14:59:48.335Z","0.0.12":"2016-06-28T15:31:32.077Z","0.0.13":"2016-09-21T13:19:35.281Z","0.0.14":"2016-10-19T14:52:15.068Z","0.0.15":"2016-10-24T11:17:42.382Z","0.0.16":"2016-11-09T22:11:50.437Z","0.0.17":"2016-11-21T16:06:54.128Z","0.0.18":"2016-11-22T14:17:10.560Z","0.0.19":"2016-12-06T10:44:01.777Z","0.0.20":"2016-12-06T12:37:08.194Z","0.0.21":"2016-12-08T13:13:46.559Z","0.0.22":"2017-02-18T21:07:15.774Z","0.0.23":"2017-03-07T11:08:53.554Z","0.0.24":"2017-03-16T15:22:36.878Z","0.0.25":"2017-07-10T14:24:07.050Z","0.0.26":"2017-07-14T10:32:19.213Z","0.0.27":"2017-07-24T13:28:25.939Z","0.0.28":"2017-11-01T10:40:40.745Z","0.0.29":"2017-11-03T15:51:38.622Z"},"keywords":["cttv","tnt","genome","browser","snps","variation","disease","biojs"],"repository":{"type":"git","url":"https://github.com/CTTV/targetGenomeBrowser"},"author":{"name":"Miguel Pignatelli"},"license":"Apache-2.0","readmeFilename":"README.md"}