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Merge pull request #79 from ebi-uniprot/new-aa-scores
New aa scores
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| export function Info(props: {text?: string}) { | ||
| if (props.text === null) | ||
| return <></> | ||
| return <div className="info" title={props.text}></div> | ||
| } | ||
|
|
||
| export const pubmedRef = (id: number) => { | ||
| return <sup><a href={`http://www.ncbi.nlm.nih.gov/pubmed/${id}`} target="_blank" | ||
| rel="noreferrer" title={`Source: PubMed ID ${id}`}>ref</a></sup> | ||
| } |
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24 changes: 13 additions & 11 deletions
24
src/ui/components/function/prediction/AlphaMissensePred.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,58 @@ | ||
| import tinygradient from "tinygradient"; | ||
| import {ESMScore} from "../../../../types/MappingResponse"; | ||
| import {getPredRef, PredAttr, PUBMED_ID} from "./Prediction"; | ||
| import { | ||
| PredAttr, | ||
| PUBMED_ID | ||
| } from "./Prediction"; | ||
| import Spaces from "../../../elements/Spaces"; | ||
| import {STD_BENIGN_COLOR, STD_COLOR_GRADIENT, STD_PATHOGENIC_COLOR, STD_UNCERTAIN_COLOR} from "./PredConstants"; | ||
| import {Info, pubmedRef} from "../../common/Common"; | ||
|
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| // James: A score of -7.5 appears to be used for pathogenicity in ESM1b. I am not sure we can say that 0--7.5 is benign though. | ||
| // Perhaps just leave those blank for now and just label the ones -7.5 and below. | ||
| // likely pathogenic (yellow) -25 <------> 0 likely benign (blue) | ||
| export const ESM_SCORE_ATTR: PredAttr[] = [ | ||
| {color: '#460556', title: 'pathogenic' }, | ||
| {color: '#218c8f', title: '' }, | ||
| {color: '#f9e725', title: '' } // maybe benign | ||
| {color: '#460556', stdColor: STD_BENIGN_COLOR , title: 'benign', info: '-5 to 0 likely benign' }, | ||
| {color: '#218c8f', stdColor: STD_UNCERTAIN_COLOR, title: 'uncertain', info: '-10 to -5 uncertain significance' }, | ||
| {color: '#f9e725', stdColor: STD_PATHOGENIC_COLOR, title: 'pathogenic', info: '-25 to -10 likely pathogenic' } | ||
| ] | ||
|
|
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| export const ESM_MAX_SCORE = -25 | ||
| export const ESM_PATHOGENIC_SCORE = -7.5 | ||
|
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| export const ESM_COLOUR_GRADIENT = tinygradient(ESM_SCORE_ATTR.map(s => s.color)); | ||
| export const ESM_COLOR_GRADIENT = tinygradient(ESM_SCORE_ATTR.map(s => s.color)); | ||
|
|
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| export const EsmPred = (props: { esm?: ESMScore }) => { | ||
| export const EsmPred = (props: { esm?: ESMScore, stdColor: boolean }) => { | ||
| if (props.esm === undefined || props.esm === null) { | ||
| return <></> | ||
| } | ||
| return <div className="aa-pred"> | ||
| <div>ESM-1b {getPredRef(PUBMED_ID.ESM)}</div> | ||
| <div>ESM-1b {pubmedRef(PUBMED_ID.ESM)}</div> | ||
| <div>{props.esm.score}</div> | ||
| <div><EsmPredIcon esmScore={props.esm}/></div> | ||
| <div><EsmPredIcon {...props}/></div> | ||
| </div> | ||
| } | ||
|
|
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| function EsmPredIcon(props: {esmScore?: ESMScore}) { | ||
| if (props.esmScore) { | ||
| let title = ''; | ||
| if (props.esmScore.score < ESM_PATHOGENIC_SCORE) { | ||
| title = ESM_SCORE_ATTR[0].title | ||
| } | ||
| const colorAtPos = ESM_COLOUR_GRADIENT.rgbAt(props.esmScore.score/ ESM_MAX_SCORE).toHexString() | ||
| function EsmPredIcon(props: {esm?: ESMScore, stdColor: boolean }) { | ||
| if (props.esm) { | ||
| const colorGrad = props.stdColor ? STD_COLOR_GRADIENT : ESM_COLOR_GRADIENT; | ||
| const colorAtPos = colorGrad.rgbAt(props.esm.score/ ESM_MAX_SCORE).toHexString() | ||
| const esmAttr = esmScoreAttr(props.esm.score) | ||
| return <> | ||
| <i className="bi bi-circle-fill" style={{color: colorAtPos}}></i> | ||
| <Spaces/>{title} | ||
| <Spaces/>{esmAttr && <> | ||
| {esmAttr.title} | ||
| <Info text={esmAttr.info}/> | ||
| </>} | ||
| </> | ||
| } | ||
| return <></> | ||
| } | ||
|
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| function esmScoreAttr(score: number) { | ||
| if (score >= -5 && score < 0) { | ||
| return ESM_SCORE_ATTR[0] | ||
| } else if (score >= -10 && score < -5) { | ||
| return ESM_SCORE_ATTR[1] | ||
| } else if (score >= -25 && score < -10) { | ||
| return ESM_SCORE_ATTR[2] | ||
| } | ||
| return null | ||
| } |
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