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reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["bioinformatics","d3","information-theory","react","react-components","reactjs","sequence-logo"],"created_at":"2024-10-05T18:04:45.540Z","updated_at":"2026-02-13T22:01:31.777Z","avatar_url":"https://github.com/alexpreynolds.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# react-seqlogo\n\nThis React component renders [residue sequence logos](https://en.wikipedia.org/wiki/Sequence_logo) from a structured Javascript object (described below) containing [FASTA-formatted sequences](https://en.wikipedia.org/wiki/FASTA_format), or a string containing a [MEME motif table](http://meme-suite.org/doc/meme-format.html). This component can also be used to render an [Epilogos](https://epilogos.altiusinstitute.org) stacked bar-chart of chromatin state logos from [Epilogos-MEME](https://epilogos-meme.altiusinstitute.org) table data.\n\n\n## Installation\n\nIn your React project, install the `react-seqlogo` package:\n\n```\n$ npm install react-seqlogo\n```\n\nThis package is hosted from [NPM](https://www.npmjs.com/package/react-seqlogo). Source is available at [Github](https://github.com/alexpreynolds/react-seqlogo).\n\n## Usage\n\nAdd a sequence logo to your React application with desired properties:\n\n```\nimport SequenceLogo from 'react-seqlogo';\n\n...\n\n\u003cSequenceLogo props... /\u003e\n```\n\n## Demo\n\nThis project includes a demo frontend that shows how one could use this component:\n\n```\n$ npm run start\n```\n\nOnce the server has initialized, open a web browser and visit: http://localhost:8080\n\n## Properties\n\nAvailable properties (and their default values or options) for the main `\u003cSequenceLogo /\u003e` component include:\n\n```\n{\n  title           : '',\n  mode            : 'FASTA' | 'MEMEMotif',\n  colorScheme     : 'base_pairing' |\n                    'charge' | \n                    'chemistry' | \n                    'classic' | \n                    'epilogos-15state-human' | \n                    'epilogos-18state-human' | \n                    'epilogos-25state-human' | \n                    'epilogos-15state-mouse' | \n                    'hydrophobicity' | \n                    'nucleotide' | \n                    'taylor',\n  item            : {} | '',\n  type            : 'nucleotide' | 'protein' | 'epilogos',\n  yAxisTicks      : 2,\n  svgWidth        : 600,\n  svgHeight       : 300,\n  svgLetterWidth  : 510,\n  svgLetterHeight : 210,\n  svgMargin : { \n    top    : 20,\n    right  : 0,\n    bottom : 10,\n    left   : 25\n  }, \n}\n```\n\n## Rendering\n\nAt minimum, an `item` is needed to turn into a sequence logo. The `item` property ultimately provides the base counts needed to render a logo, either in the form of raw sequences or letter frequencies.\n\nAn `item` may be a structured Javascript object containing FASTA-formatted sequences or a string containing a MEME motif table, depending on the specified `mode`. \n\nThe logo that results will be colored and rendered with attributes and rules derived from the `colorScheme` and `type` properties.\n\n### FASTA\n\nVery simply, an `item` is a pairing of an `identifier` string and a `sequences` string:\n\n```\n{\n  identifier : '',\n  sequences : ''\n}\n```\n\nFor example:\n\n```\n{\n  identifier : '3 ad-hoc RNA sequences',\n  sequences : `\u003eseq001\nCUUAUAUCCUUACC\n\u003eseq002\nCUCGCGUGUCAAUC\n\u003eseq003\nCTCCCGUUGCAAUC\n`\n}\n```\n\nThe `sequences` string is more familiar as the contents of a generic, multiline FASTA file. The `identifier` gives the sequences a usable title.\n\n### MEME motif\n\nA MEME motif is a string contains metadata describing the item and the letter-probability matrix, which is turned into a sequence logo. The format of this string is defined [here](http://meme-suite.org/doc/meme-format.html).\n\n## Issues\n\nAt this time, there are rendering problems with residues in protein sequence logos.\n\nAlso, not all features of [WebLogo 3](http://weblogo.threeplusone.com/) are supported. Future versions may add support for alternate units such as probability density and nats, error bars, logo range subsets and offsets, and background composition correction.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Freact-seqlogo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falexpreynolds%2Freact-seqlogo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Freact-seqlogo/lists"}