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| GNU LESSER GENERAL PUBLIC LICENSE | ||
| Version 3, 29 June 2007 | ||
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| [](https://travis-ci.org/cBioPortal/oncoprintjs) | ||
| # OncoprintJS | ||
| This is the library that generates the Oncoprint visualization in cBioPortal. Essentially, it populates a canvas of a grid of `m` tracks of `n` types, where each element can either be a discrete value represented by a colored glyph on a grey background or a continuous value within a color range. Oncoprint can have many conceivable uses, but in cBioPortal, it is primarily used to visualize tracks of `m` genes and `n` patient samples, where the colored glyphs represent genomic alterations. It is also used to display a heatmap of gene and/or protein expression values for those `m` genes and `n` patient samples. | ||
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| ## Using the Node Module | ||
| Oncoprint is on [NPM](https://www.npmjs.com/package/oncoprintjs). To install: | ||
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| npm install --save oncoprintjs | ||
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| In order to use it, just `require` it into your script. | ||
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| const Oncoprint = require('oncoprintjs'); | ||
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| It can also be imported | ||
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| import Oncoprint from "oncoprintjs"; | ||
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| A full documentation of the API is still pending, but the typescript declarations in `dist/js/oncoprint.d.ts` may be of use. | ||
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| ## Development | ||
| ### Getting Started | ||
| First, clone the repo: | ||
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| git clone https://github.com/cBioPortal/oncoprintjs.git | ||
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| Install the necessary NPM packages defined in `package.json` by running: | ||
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| npm install | ||
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| Next, build | ||
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| npm run build | ||
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| Which will write `dist/oncoprint.bundle.js`, which is a CommonJS module and can be included using `require`, or `import`. | ||
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| The directory `rules/` contains glyph styling specifications that are specific to the genomic alterations use case of Oncoprint, which you may want to use. | ||
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| ### Using a local version of oncoprintjs during development (e.g. in cBioPortal) | ||
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| yalc (https://github.com/wclr/yalc) is extremely useful for this. | ||
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| Whenever you have made a change to oncoprintjs you want to bring into another package: | ||
| (1) First navigate to the oncoprint directory. Then build: | ||
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| npm run build | ||
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| (2) Then "publish" the package locally using yalc | ||
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| yalc publish | ||
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| (3) Now go to the directory of your project (e.g. cbioportal-frontend), and add the local package | ||
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| yalc add oncoprintjs | ||
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| (4) Install packages again, using npm or yarn. Now, you will be using your local version of oncoprintjs. | ||
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| (5) When you no longer want to be using the local version of oncoprintjs, simply run | ||
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| yalc remove oncoprintjs | ||
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| And run npm or yarn again. | ||
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| ### Changes to Oncoprint | ||
| If you make changes to the Oncoprint code base and want to load it into the examples, do not modify `oncoprint.bundle.js`, since all of your code will get overwritten when compiled using `npm run build`. Instead, modify the files in `src/` and then re-run `npm run build`. | ||
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| ### Schematic diagrams | ||
| oncoprintjs is written loosely with a Model-View-Controller framework, although some Views definitely have their own state. | ||
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| import config from '../config/jest.config'; | ||
| export default config; |
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