Add AlphaMissense in Functional prediction #160
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| import * as React from 'react'; | ||
| import { DefaultTooltip } from 'cbioportal-frontend-commons'; | ||
| import { makeObservable } from 'mobx'; | ||
| import functionalGroupsStyle from '../functionalGroups.module.scss'; | ||
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| export interface IAlphaMissenseProps { | ||
| amClass?: string; | ||
| amPathogenicityScore?: number; | ||
| } | ||
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| const ALPHAMISSENSE_URL = 'https://www.science.org/doi/10.1126/science.adg7492'; | ||
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| const AlphaMissenseInfo: React.FunctionComponent = () => { | ||
| return ( | ||
| <div> | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| AlphaMissense | ||
| </a>{' '} | ||
| uses deep learning to assess the pathogenicity of missense variants, | ||
| indicating how they might affect gene function and contribute to | ||
| disease. | ||
| <div> | ||
| <b>Scores:</b> | ||
| <ul> | ||
| <li> | ||
| <b>Pathogenic:</b> Score > 0.564 – likely to cause | ||
| disease. | ||
| </li> | ||
| <li> | ||
| <b>Benign:</b> Score < 0.34 – unlikely to cause | ||
| disease. | ||
| </li> | ||
| <li> | ||
| <b>Ambiguous:</b> Score between 0.34 and 0.564 – unclear | ||
| impact; insufficient data. | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| </div> | ||
| ); | ||
| }; | ||
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| export default class AlphaMissense extends React.Component< | ||
| IAlphaMissenseProps, | ||
| {} | ||
| > { | ||
| constructor(props: IAlphaMissenseProps) { | ||
| super(props); | ||
| makeObservable(this); | ||
| } | ||
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| public render() { | ||
| let alphaMissenseContent: JSX.Element; | ||
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| const dataSource = ( | ||
| <> | ||
| AlphaMissense | ||
| <i className="fas fa-external-link-alt" /> | ||
| </> | ||
| ); | ||
| if (this.props.amClass) { | ||
| alphaMissenseContent = ( | ||
| <p> | ||
| {this.props.amClass + ' '}({this.props.amPathogenicityScore} | ||
| ) | ||
| </p> | ||
| ); | ||
| } else { | ||
| alphaMissenseContent = <span> N/A </span>; | ||
| } | ||
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| return ( | ||
| <div className={functionalGroupsStyle['functional-group']}> | ||
| <div className={functionalGroupsStyle['data-source']}> | ||
| <DefaultTooltip | ||
| placement="top" | ||
| overlay={ | ||
| <div style={{ maxWidth: 450 }}> | ||
| <AlphaMissenseInfo /> | ||
| </div> | ||
| } | ||
| > | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {dataSource} | ||
| </a> | ||
| </DefaultTooltip> | ||
| </div> | ||
| <div> | ||
| <span className={functionalGroupsStyle['data-with-link']}> | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {alphaMissenseContent} | ||
| </a> | ||
| </span> | ||
| </div> | ||
| </div> | ||
| ); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,12 @@ | ||
| export const SHOW_MUTATION_ASSESSOR = true; | ||
| export const SHOW_ALPHAMISSENSE = true; | ||
| export function annotationQueryFields() { | ||
| const fields = DEFAULT_ANNOTATION_QUERY_FIELDS; | ||
| if (SHOW_MUTATION_ASSESSOR) { | ||
| fields.push('mutation_assessor'); | ||
| } | ||
| return fields; | ||
| } | ||
| export const DEFAULT_ANNOTATION_QUERY_FIELDS = [ | ||
| 'hotspots', | ||
| 'annotation_summary', | ||
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@@ -4260,15 +4260,10 @@ caniuse-db@^1.0.30000529, caniuse-db@^1.0.30000634, caniuse-db@^1.0.30000639: | |
| resolved "https://registry.yarnpkg.com/caniuse-db/-/caniuse-db-1.0.30000985.tgz#208c723beb15123eb27cc6ad9bc285b4f27a3f87" | ||
| integrity sha512-1m3CC9+dYNh/FHd0V1/McOB73CxjmzzrcXi360x8mKoApUY8QIOYXg4bU5QeJmlenn++20GBI38EKw6qQpJ3kQ== | ||
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| caniuse-lite@^1.0.0, caniuse-lite@^1.0.30000981, caniuse-lite@^1.0.30000984, caniuse-lite@^1.0.30001035, caniuse-lite@^1.0.30001109, caniuse-lite@^1.0.30001219: | ||
| version "1.0.30001643" | ||
| resolved "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001643.tgz" | ||
| integrity sha512-ERgWGNleEilSrHM6iUz/zJNSQTP8Mr21wDWpdgvRwcTXGAq6jMtOUPP4dqFPTdKqZ2wKTdtB+uucZ3MRpAUSmg== | ||
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| canvg@1.5.3: | ||
| version "1.5.3" | ||
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@@ -7038,10 +7033,10 @@ gauge@~2.7.3: | |
| strip-ansi "^3.0.1" | ||
| wide-align "^1.1.0" | ||
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| genome-nexus-ts-api-client@1.1.33: | ||
| version "1.1.33" | ||
| resolved "https://registry.yarnpkg.com/genome-nexus-ts-api-client/-/genome-nexus-ts-api-client-1.1.33.tgz#aea3eafe6ca59e0187c25c487b7fb9f9b704bdde" | ||
| integrity sha512-wrbDKoVjw9etDChfacrNStlORqWlS/k2dA5DzlxFEfen3WYO7QtXAFLVSxpjanA/3sGQnVqaxreZzjTPDXhs1A== | ||
| dependencies: | ||
| superagent "^3.8.3" | ||
| typescript "4.0.3" | ||
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@@ -7054,6 +7049,14 @@ genome-nexus-ts-api-client@^1.1.28: | |
| superagent "^3.8.3" | ||
| typescript "4.0.3" | ||
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| genome-nexus-ts-api-client@^1.1.32: | ||
| version "1.1.32" | ||
| resolved "https://registry.yarnpkg.com/genome-nexus-ts-api-client/-/genome-nexus-ts-api-client-1.1.32.tgz#e8a9c70d6644e17ae7f76c803ecb0d3e1720c7d9" | ||
| integrity sha512-ELXH+50alvUVnRioxCOLvxf5VcN57YVheF80kEVFBXT5cnO178tvDLHdaqbmAlEvezHwptercQ9kqh8d9TTm5Q== | ||
| dependencies: | ||
| superagent "^3.8.3" | ||
| typescript "4.0.3" | ||
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| gensync@^1.0.0-beta.1: | ||
| version "1.0.0-beta.2" | ||
| resolved "https://registry.yarnpkg.com/gensync/-/gensync-1.0.0-beta.2.tgz#32a6ee76c3d7f52d46b2b1ae5d93fea8580a25e0" | ||
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we need this import. sorry for the confusion.