Skip to content

Commit

Permalink
level added
Browse files Browse the repository at this point in the history
  • Loading branch information
@chinmehta
chinmehta committed Nov 7, 2023
1 parent 34e8587 commit 1e4c9c4
Show file tree
Hide file tree
Showing 5 changed files with 366 additions and 256 deletions.
7 changes: 7 additions & 0 deletions packages/sections/src/constants.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,13 @@ export const colorRange = [
"#005299",
];

export const PHARM_GKB_COLOR = {
green: "#0ABC72",
blue: "#2A74DF",
yellow: "#FFC105",
red: "#C53B3B",
};

export const defaultRowsPerPageOptions = [10, 25, 100];

export const decimalPlaces = 3;
Expand Down
317 changes: 186 additions & 131 deletions packages/sections/src/drug/Pharmacogenomics/Body.jsx
View file
Original file line number Diff line number Diff line change
@@ -1,152 +1,207 @@
import classNames from "classnames";
import { useQuery } from "@apollo/client";
import { makeStyles } from "@mui/styles";
import { Link, SectionItem, Tooltip, DataTable, LabelChip, PublicationsDrawer } from "ui";

import { epmcUrl } from "../../utils/urls";
import { definition } from ".";
import Description from "./Description";
import PHARMACOGENOMICS_QUERY from "./Pharmacogenomics.gql";
import { naLabel, defaultRowsPerPageOptions } from "../../constants";
import { naLabel, defaultRowsPerPageOptions, PHARM_GKB_COLOR } from "../../constants";

const columns = [
{
id: "gene",
label: "Gene",
renderCell: ({ targetFromSourceId }) =>
targetFromSourceId ? (
<Link
tooltip="This gene may not be direct target of the drug."
to={`/target/${targetFromSourceId}`}
>
<span>{targetFromSourceId}</span>
</Link>
) : (
naLabel
),
const useStyles = makeStyles(theme => ({
level: {
color: "white",
padding: theme.spacing(0.5),
borderRadius: theme.spacing(0.5),
},
{
id: "rsId",
label: "RsID",
renderCell: ({ variantRsId }) => variantRsId || naLabel,
green: {
background: PHARM_GKB_COLOR.green,
},
{
id: "genotypeId",
label: "Genotype ID",
renderCell: ({ genotypeId }) =>
genotypeId ? (
<Tooltip
title={
<>
VCF-style(chr_pos_ref_allele1,allele2). See
<Link
external
to="https://github.com/apriltuesday/opentargets-pharmgkb/tree/issue-18#variant-coordinate-computation"
>
{" "}
here{" "}
</Link>
for more details
</>
}
>
<span>{genotypeId}</span>
</Tooltip>
) : (
naLabel
),
},
{
id: "variantFunctionalConsequence",
label: "Variant Consequence",
renderCell: ({ variantFunctionalConsequence }) => {
if (variantFunctionalConsequence)
return (
<LabelChip
label={variantFunctionalConsequence.id}
value={variantFunctionalConsequence.label}
tooltip="Ensembl variant effect predictor"
/>
);
return naLabel;
},
red: {
background: PHARM_GKB_COLOR.red,
},
{
id: "drugResponse",
label: "Drug Response",
renderCell: ({ phenotypeText = naLabel, phenotypeFromSourceId, genotypeAnnotationText }) => {
const phenotypeTextElement = phenotypeFromSourceId ? (
<Link tooltip={genotypeAnnotationText} to={`/disease/${phenotypeFromSourceId}`}>
{phenotypeText}
</Link>
) : (
<Tooltip title={genotypeAnnotationText}>{phenotypeText}</Tooltip>
);
return phenotypeTextElement;
},
yellow: {
background: PHARM_GKB_COLOR.yellow,
},
{
id: "drugResponseCategory",
label: "Drug Response Category",
renderCell: ({ pgxCategory }) => pgxCategory || naLabel,
blue: {
background: PHARM_GKB_COLOR.blue,
},
{
id: "confidenceLevel",
label: "Confidence (Level)",
renderCell: ({ evidenceLevel }) =>
evidenceLevel ? (
<Tooltip
title={
<>
As defined by
<Link external to={`https://www.pharmgkb.org/page/clinAnnLevels`}>
{" "}
PharmGKB ClinAnn Levels
}));

const getLevelElementClassName = level => {
switch (level) {
case "1":
return "green";
case "1A":
return "green";
case "2":
return "level-blue";
case "2A":
return "level-blue";
case "3":
return "level-yellow";
case "4":
return "level-red";
default:
return "level-red";
}
};

function Body({ id: chemblId, label: name, entity }) {
const variables = { chemblId };
const classes = useStyles();

const columns = [
{
id: "gene",
label: "Gene",
renderCell: ({ targetFromSourceId, isDirectTarget }) => {
if (targetFromSourceId) {
const tooltipText = isDirectTarget
? "The variant is in the drug's primary target gene."
: "The variant is outside the drug's primary target gene.";
return (
<Tooltip title={tooltipText} showHelpIcon>
<Link to={`/target/${targetFromSourceId}`}>
<span>{targetFromSourceId}</span>
</Link>
</>
}
>
<span>{evidenceLevel}</span>
</Tooltip>
) : (
naLabel
),
},
{
id: "source",
label: "Source",
renderCell: ({ studyId }) =>
studyId ? (
<Link external to={`https://www.pharmgkb.org/clinicalAnnotation/${studyId}`}>
PharmGKB-{studyId}
</Link>
) : (
naLabel
),
},
{
id: "literature",
label: "Literature",
renderCell: ({ literature }) => {
const literatureList =
literature?.reduce((acc, id) => {
if (id === "NA") return acc;
</Tooltip>
);
}
return naLabel;
},
},
{
id: "rsId",
label: "rsID",
renderCell: ({ variantRsId }) => variantRsId || naLabel,
},
{
id: "genotypeId",
label: "Genotype ID",
renderCell: ({ genotypeId }) =>
genotypeId ? (
<Tooltip
showHelpIcon
title={
<>
VCF-style(chr_pos_ref_allele1,allele2). See
<Link
external
to="https://github.com/apriltuesday/opentargets-pharmgkb/tree/issue-18#variant-coordinate-computation"
>
{" "}
here{" "}
</Link>
for more details
</>
}
>
<span>{genotypeId}</span>
</Tooltip>
) : (
naLabel
),
},
{
id: "variantFunctionalConsequence",
label: "Variant Consequence",
renderCell: ({ variantFunctionalConsequence }) => {
if (variantFunctionalConsequence)
return (
<LabelChip
label={variantFunctionalConsequence.id}
value={variantFunctionalConsequence.label}
tooltip="Ensembl variant effect predictor"
/>
);
return naLabel;
},
},
{
id: "drugResponse",
label: "Drug Response",
renderCell: ({ phenotypeText = naLabel, phenotypeFromSourceId, genotypeAnnotationText }) => {
const phenotypeTextElement = phenotypeFromSourceId ? (
<Tooltip title={genotypeAnnotationText} showHelpIcon>
<Link to={`/disease/${phenotypeFromSourceId}`}>{phenotypeText}</Link>
</Tooltip>
) : (
<Tooltip showHelpIcon title={genotypeAnnotationText}>
{phenotypeText}
</Tooltip>
);
return phenotypeTextElement;
},
},
{
id: "drugResponseCategory",
label: "Drug Response Category",
renderCell: ({ pgxCategory }) => pgxCategory || naLabel,
},
{
id: "confidenceLevel",
label: "Confidence (Level)",
renderCell: ({ evidenceLevel }) => {
if (evidenceLevel) {
const levelClass = getLevelElementClassName(evidenceLevel);
return (
<Tooltip
title={
<span>
As defined by
<Link external to={`https://www.pharmgkb.org/page/clinAnnLevels`}>
{" "}
PharmGKB ClinAnn Levels
</Link>
</span>
}
>
<span className={classNames(classes.level, classes[levelClass])}>
Level {evidenceLevel}
</span>
</Tooltip>
);
}
return naLabel;
},
},
{
id: "source",
label: "Source",
renderCell: ({ studyId }) =>
studyId ? (
<Link external to={`https://www.pharmgkb.org/clinicalAnnotation/${studyId}`}>
PharmGKB
</Link>
) : (
naLabel
),
},
{
id: "literature",
label: "Literature",
renderCell: ({ literature }) => {
const literatureList =
literature?.reduce((acc, id) => {
if (id === "NA") return acc;

return [
...acc,
{
name: id,
url: epmcUrl(id),
group: "literature",
},
];
}, []) || [];
return [
...acc,
{
name: id,
url: epmcUrl(id),
group: "literature",
},
];
}, []) || [];

return <PublicationsDrawer entries={literatureList} />;
return <PublicationsDrawer entries={literatureList} />;
},
},
},
];
];

function Body({ id: chemblId, label: name, entity }) {
const variables = { chemblId };
const request = useQuery(PHARMACOGENOMICS_QUERY, {
variables,
});
Expand Down
1 change: 1 addition & 0 deletions packages/sections/src/drug/Pharmacogenomics/Pharmacogenomics.gql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ query PharmacogenomicsQuery($chemblId: String!) {
id
label
}
isDirectTarget
phenotypeFromSourceId
genotypeAnnotationText
phenotypeText
Expand Down
6 changes: 2 additions & 4 deletions packages/sections/src/target/Pharmacogenomics/Pharmacogenomics.gql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,8 @@ query PharmacogenomicsQuery($ensemblId: String!) {
id
label
}
drug {
id
name
}
drugFromSource
drugId
phenotypeFromSourceId
genotypeAnnotationText
phenotypeText
Expand Down
Loading

0 comments on commit 1e4c9c4

Please sign in to comment.