From 686aa4c0091f035c0c6cf7751debfbcd95d77d53 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 13:25:10 -0500 Subject: [PATCH 01/25] KPMP-4435: RP Viz tables --- src/components/DataViz/RegionalProteomics.js | 145 +++++++++++++++---- src/helpers/ApolloClient.js | 68 +++++++++ 2 files changed, 185 insertions(+), 28 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 48dc7124..9f485e91 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -1,42 +1,131 @@ import React, { Component } from 'react'; -import { Container, Row, Col } from 'reactstrap'; +import {Container, Row, Col, ButtonGroup, Button} from 'reactstrap'; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import DataTypeSelectorContainer from './DataTypeSelectorContainer'; -import { faShare } from "@fortawesome/free-solid-svg-icons"; +import {faDownload, faShare} from "@fortawesome/free-solid-svg-icons"; import queryString from 'query-string'; +import {fetchRegionalTranscriptomics} from "../../helpers/ApolloClient"; +import LMDDotPlot from "../Plots/LMDDotPlot"; +import RegionalProteomicsTable from "../ExpressionTables/RegionalProteomicsTable"; +import {formatTissueType} from "../../helpers/Utils"; +import {CSVLink} from "react-csv"; +import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { - constructor(props) { - super(props); - this.state = { rpAllPlotData: [], rpAllTableData: [], rpGTPlotData: [], rpGTTableData: [], selectedComparison: 'all_segments', selectedPlot: 'box' }; - const queryParam = queryString.parse(props.location.search); - if (!this.props.tissueType) { - this.props.setTissueType('all') - } - if (queryParam && queryParam.dataType) { - this.props.resetState(); - props.setDataType('rp'); - window.open(props.location.pathname, '_self'); - } -}; + constructor(props) { + super(props); + this.state = { rpAllPlotData: [], rpAllTableData: [] }; + const queryParam = queryString.parse(props.location.search); + if (!this.props.tissueType) { + this.props.setTissueType('all') + } + if (queryParam && queryParam.dataType) { + this.props.resetState(); + props.setDataType('rp'); + window.open(props.location.pathname, '_self'); + } + }; + + componentDidMount() { + if (this.props.gene.symbol) { + this.getRPData(); + } + }; + + componentDidUpdate(prevProps, prevState, snapShot) { + if (this.props.tissueType !== prevProps.tissueType) { + this.setState({ rpAllTableData: this.state.rpAllPlotData[this.props.tissueType] }); + } + if (this.props.gene !== prevProps.gene) { + this.getRPData(); + } + }; + + getRPData = () => { + fetchRegionalTranscriptomics(this.props.gene.symbol).then((result) => { + this.setState({ rpAllPlotData: result }); + this.setState({ rpAllTableData: result[this.props.tissueType] }); + } + ); + }; + render() { + let plot = {}; + let table = {}; + table = ; + plot = return (
- -
- - - - - -
Gene Expression:
-

Enter a gene above to get started

- - -
- + {!this.props.gene.symbol ? + +
+ + + + + +
Gene Expression:
+

Enter a gene above to get started

+ + +
+ + : + + +
{this.props.gene.symbol} expression comparison across regions + in {formatTissueType(this.props.tissueType)}
+
+ + + + + Display by: + + + + + + {plot} +
+ + + + + The comparisons in the plot and data table were performed across different + segments in the same condition. The plot data should be read and interpreted + following the horizontal guides. The fold change and significance of a segment are + related to the average expression of all segments in the same condition. Due to + the experiment design, it is not possible to draw direct comparisons in the same + segment across conditions. + + + + + +
{this.props.gene.symbol} expression comparison across regions + in {formatTissueType(this.props.tissueType)}
+
NS = Not Significant
+ + + handleGoogleAnalyticsEvent('Explorer', 'Download', this.getExportFilename())} + data={cleanDownloadData} + filename={this.getExportFilename()} + target="_blank" + className="text-body icon-container" + > + + + + + + {table} + + + }
) diff --git a/src/helpers/ApolloClient.js b/src/helpers/ApolloClient.js index f1b773ad..dde2dbd6 100644 --- a/src/helpers/ApolloClient.js +++ b/src/helpers/ApolloClient.js @@ -319,6 +319,74 @@ export const fetchRegionalTranscriptomics = async (comparisonType, geneSymbol) = }; +export const fetchRegionalProteomics = async (geneSymbol) => { + let query = gql` + query { + getRPGeneExpressionByTissue(geneSymbol: "${geneSymbol}") { + aki { + id + segment + segmentName + geneSymbol + pVal + foldChange + pValLog10 + stdDev + sampleCount + tissueType + } + ckd { + id + segment + segmentName + geneSymbol + pVal + foldChange + pValLog10 + stdDev + sampleCount + tissueType + } + all { + id + segment + segmentName + geneSymbol + pVal + foldChange + pValLog10 + stdDev + sampleCount + tissueType + } + hrt { + id + segment + segmentName + geneSymbol + pVal + foldChange + pValLog10 + stdDev + sampleCount + tissueType + } + } + }`; + + const response = await apolloClient.query({ + query: query, + fetchPolicy: 'cache-first' + }); + + if (response.data && response.data.getRPGeneExpressionByTissue) { + return response.data.getRPGeneExpressionByTissue; + } else { + store.dispatch(sendMessageToBackend("Could not retrieve regional proteomics data: " + response.error)); + } + +}; + export const fetchRegionalTranscriptomicsByStructure = async (structure) => { let query = gql` query { From e734261ecc7ef37063352d8066d65631b52d1005 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 13:41:26 -0500 Subject: [PATCH 02/25] KPMP-4435: Comment out unused stuff for now --- src/components/DataViz/RegionalProteomics.js | 14 +-- .../RegionalProteomicsTable.js | 89 +++++++++++++++++++ 2 files changed, 92 insertions(+), 11 deletions(-) create mode 100644 src/components/ExpressionTables/RegionalProteomicsTable.js diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 9f485e91..7320d3e0 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -52,7 +52,7 @@ class RegionalProteomics extends Component { render() { let plot = {}; let table = {}; - table = ; + // table = ; plot = return (
@@ -110,19 +110,11 @@ class RegionalProteomics extends Component {
NS = Not Significant
- handleGoogleAnalyticsEvent('Explorer', 'Download', this.getExportFilename())} - data={cleanDownloadData} - filename={this.getExportFilename()} - target="_blank" - className="text-body icon-container" - > - - + {"download link goes here"} - {table} + {"table goes here"} } diff --git a/src/components/ExpressionTables/RegionalProteomicsTable.js b/src/components/ExpressionTables/RegionalProteomicsTable.js new file mode 100644 index 00000000..1be3dfe6 --- /dev/null +++ b/src/components/ExpressionTables/RegionalProteomicsTable.js @@ -0,0 +1,89 @@ +import React, {Component} from "react"; + +import { AgGridColumn, AgGridReact } from 'ag-grid-react'; +import {Col} from "reactstrap"; +import 'ag-grid-community/dist/styles/ag-grid.css'; +import 'ag-grid-community/dist/styles/ag-theme-alpine.css'; +import 'ag-grid-community/dist/styles/ag-theme-bootstrap.css'; +import 'ag-grid-community/dist/styles/ag-theme-material.css'; +import 'ag-grid-community/dist/styles/ag-theme-balham.css'; +import { formatNumberToPrecision } from "../../helpers/Utils"; +import {FontAwesomeIcon} from "@fortawesome/react-fontawesome"; +import {faInfoCircle} from "@fortawesome/free-solid-svg-icons"; + +class CustomHeader extends Component { + + render() { + return ( + + {this.props.displayName}   + + + + + ) + } +} + +class CustomTooltip extends Component { + + getReactContainerClasses() { + return ['custom-tooltip']; + } + + render() { + let isHeader = this.props.rowIndex === undefined; + return ( + + {isHeader &&
{this.props.tooltipText}
} + + ) + } + +} + +class RegionalProteomicsTable extends Component { + + numberFormatter = (params) => { + return formatNumberToPrecision(params.value, 3) + }; + + render() { + return ( + + +
+ + + + + + + + +
+ + + ) + } + +} + +export default RegionalTranscriptomicsTable; \ No newline at end of file From 54316bbdbb1b863faf2f6d9d55f8863e5f0563be Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 14:29:10 -0500 Subject: [PATCH 03/25] KPMP-4435: Export the right thing --- src/components/ExpressionTables/RegionalProteomicsTable.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/components/ExpressionTables/RegionalProteomicsTable.js b/src/components/ExpressionTables/RegionalProteomicsTable.js index 1be3dfe6..f8ad34c4 100644 --- a/src/components/ExpressionTables/RegionalProteomicsTable.js +++ b/src/components/ExpressionTables/RegionalProteomicsTable.js @@ -86,4 +86,4 @@ class RegionalProteomicsTable extends Component { } -export default RegionalTranscriptomicsTable; \ No newline at end of file +export default RegionalProteomicsTable; \ No newline at end of file From bb527482bf12c9e62bead78ca42ddf543a167fc8 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 14:38:30 -0500 Subject: [PATCH 04/25] KPMP-4435: Fetch RP --- src/components/DataViz/RegionalProteomics.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 7320d3e0..02359394 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -4,7 +4,7 @@ import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import DataTypeSelectorContainer from './DataTypeSelectorContainer'; import {faDownload, faShare} from "@fortawesome/free-solid-svg-icons"; import queryString from 'query-string'; -import {fetchRegionalTranscriptomics} from "../../helpers/ApolloClient"; +import {fetchRegionalProteomics} from "../../helpers/ApolloClient"; import LMDDotPlot from "../Plots/LMDDotPlot"; import RegionalProteomicsTable from "../ExpressionTables/RegionalProteomicsTable"; import {formatTissueType} from "../../helpers/Utils"; @@ -42,7 +42,7 @@ class RegionalProteomics extends Component { }; getRPData = () => { - fetchRegionalTranscriptomics(this.props.gene.symbol).then((result) => { + fetchRegionalProteomics(this.props.gene.symbol).then((result) => { this.setState({ rpAllPlotData: result }); this.setState({ rpAllTableData: result[this.props.tissueType] }); } From ff5453292f21573915e6f8cf5729ad6c9589d5cb Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 14:48:21 -0500 Subject: [PATCH 05/25] KPMP-4435: RP field changes --- src/components/Plots/LMDDotPlot.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/components/Plots/LMDDotPlot.js b/src/components/Plots/LMDDotPlot.js index e2b51f2b..9f5ebfb5 100644 --- a/src/components/Plots/LMDDotPlot.js +++ b/src/components/Plots/LMDDotPlot.js @@ -84,9 +84,9 @@ class LMDDotPlot extends Component { if (data) { resultArr.forEach((row) => { - xValues.push(row.segment); + xValues.push(row.segment ? row.segment : row.region); yValues.push(this.abbreviate(row.tissueType).toUpperCase()); - bubbles.push(row.pValLog10); + bubbles.push(row.pValLog10 ? row.pValLog10 : row.adjPVal); colors.push(row.foldChange); }); plotObj = { From b8ef19b72251f1834f8db6218f64c4d2c1432a89 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Thu, 30 Nov 2023 15:03:25 -0500 Subject: [PATCH 06/25] KPMP-4435: Field changes and alias --- src/helpers/ApolloClient.js | 96 +++++++++++++++++++++---------------- 1 file changed, 56 insertions(+), 40 deletions(-) diff --git a/src/helpers/ApolloClient.js b/src/helpers/ApolloClient.js index dde2dbd6..6e6969ae 100644 --- a/src/helpers/ApolloClient.js +++ b/src/helpers/ApolloClient.js @@ -324,52 +324,68 @@ export const fetchRegionalProteomics = async (geneSymbol) => { query { getRPGeneExpressionByTissue(geneSymbol: "${geneSymbol}") { aki { - id - segment - segmentName - geneSymbol - pVal - foldChange - pValLog10 - stdDev - sampleCount - tissueType + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + segment: region + foldChange + pValLog10: adjPVal + tissueType + sampleCount } ckd { - id - segment - segmentName - geneSymbol - pVal - foldChange - pValLog10 - stdDev - sampleCount - tissueType + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + segment: region + foldChange + pValLog10: adjPVal + tissueType + sampleCount } all { - id - segment - segmentName - geneSymbol - pVal - foldChange - pValLog10 - stdDev - sampleCount - tissueType + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + segment: region + foldChange + pValLog10: adjPVal + tissueType + sampleCount } hrt { - id - segment - segmentName - geneSymbol - pVal - foldChange - pValLog10 - stdDev - sampleCount - tissueType + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + segment: region + foldChange + pValLog10: adjPVal + tissueType + sampleCount } } }`; From c27c0535203f4a51ef2d997dcb6b5df6b5a11b98 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Tue, 5 Dec 2023 13:05:18 -0500 Subject: [PATCH 07/25] KPMP-4435: RP viz --- src/components/DataViz/RegionalProteomics.js | 41 ++++- src/helpers/ApolloClient.js | 149 +++++++++++-------- 2 files changed, 117 insertions(+), 73 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 02359394..d7c63fa9 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -7,14 +7,14 @@ import queryString from 'query-string'; import {fetchRegionalProteomics} from "../../helpers/ApolloClient"; import LMDDotPlot from "../Plots/LMDDotPlot"; import RegionalProteomicsTable from "../ExpressionTables/RegionalProteomicsTable"; -import {formatTissueType} from "../../helpers/Utils"; +import {convertRPResultsToMap, formatTissueType} from "../../helpers/Utils"; import {CSVLink} from "react-csv"; import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) { super(props); - this.state = { rpAllPlotData: [], rpAllTableData: [] }; + this.state = { rpAllData: [] , plotData: {}, accessionNums: [], selectedAccession: ""}; const queryParam = queryString.parse(props.location.search); if (!this.props.tissueType) { this.props.setTissueType('all') @@ -43,17 +43,41 @@ class RegionalProteomics extends Component { getRPData = () => { fetchRegionalProteomics(this.props.gene.symbol).then((result) => { - this.setState({ rpAllPlotData: result }); - this.setState({ rpAllTableData: result[this.props.tissueType] }); + this.setState({ rpAllData: result }); + this.setState({ selectedAccession: result[0].accession}); + this.mapPlotData(result); + // this.setState({ rpTableData: result[this.props.tissueType] }); } ); }; + mapPlotData = (result) => { + let plots = {}; + let accessionNums = []; + for (let {accession, rpExpressionByTissueType} in result) { + plots[accession] = rpExpressionByTissueType; + accessionNums.push(accession); + } + this.setState({ plotData: plots }); + this.setState({ accessionNums: accessionNums}) + } + + getTabGroup = (accessionNums) => { + let tabs = [] + for (let accession in accessionNums) { + tabs.push() + } + return( + {tabs} + ) + } + render() { - let plot = {}; - let table = {}; + //let plot = this.state.plotData[this.state.selectedAccession]; + //let table = {}; // table = ; - plot = + let plot = + let tabs = this.getTabGroup(this.state.accessionNums); return (
@@ -84,7 +108,8 @@ class RegionalProteomics extends Component { Display by: - + {tabs} + diff --git a/src/helpers/ApolloClient.js b/src/helpers/ApolloClient.js index 6e6969ae..2f081d10 100644 --- a/src/helpers/ApolloClient.js +++ b/src/helpers/ApolloClient.js @@ -323,72 +323,91 @@ export const fetchRegionalProteomics = async (geneSymbol) => { let query = gql` query { getRPGeneExpressionByTissue(geneSymbol: "${geneSymbol}") { - aki { - id - geneSymbol - fdrConfidence - accession - description - coveragePct - numPeptides - numUniquePeptides - comparison - segment: region - foldChange - pValLog10: adjPVal - tissueType - sampleCount - } - ckd { - id - geneSymbol - fdrConfidence - accession - description - coveragePct - numPeptides - numUniquePeptides - comparison - segment: region - foldChange - pValLog10: adjPVal - tissueType - sampleCount - } - all { - id - geneSymbol - fdrConfidence - accession - description - coveragePct - numPeptides - numUniquePeptides - comparison - segment: region - foldChange - pValLog10: adjPVal - tissueType - sampleCount + accession + rpExpressionByTissueType { + all { + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + region + foldChange + adjPVal + tissueType + sampleCount + } + hrt{ + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + region + foldChange + adjPVal + tissueType + sampleCount + } + ckd{ + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + region + foldChange + adjPVal + tissueType + sampleCount + } + dmr{ + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + region + foldChange + adjPVal + tissueType + sampleCount + } + aki{ + id + geneSymbol + fdrConfidence + accession + description + coveragePct + numPeptides + numUniquePeptides + comparison + region + foldChange + adjPVal + tissueType + sampleCount + } } - hrt { - id - geneSymbol - fdrConfidence - accession - description - coveragePct - numPeptides - numUniquePeptides - comparison - segment: region - foldChange - pValLog10: adjPVal - tissueType - sampleCount - } - } - }`; + } +}`; const response = await apolloClient.query({ query: query, From adb9d21dfae9b3f0a15cb82a73020f45b2d01e66 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Tue, 5 Dec 2023 14:34:14 -0500 Subject: [PATCH 08/25] KPMP-4435: loop --- package-lock.json | 151 ++----------------- src/components/DataViz/RegionalProteomics.js | 6 +- 2 files changed, 18 insertions(+), 139 deletions(-) diff --git a/package-lock.json b/package-lock.json index 21d3fbc3..891b7693 100644 --- a/package-lock.json +++ b/package-lock.json @@ -36,7 +36,7 @@ "history": "5.0.0", "html-react-parser": "1.4.0", "isomorphic-unfetch": "3.1.0", - "kpmp-common-components": "1.2.3", + "kpmp-common-components": "1.2.7", "kpmp-common-styles": "1.0.13", "material-table": "1.69.3", "npm-run-all": "4.1.5", @@ -52,7 +52,7 @@ "react-router-dom": "5.2.0", "react-scripts": "5.0.1", "react-select": "4.0.0", - "reactstrap": "8.9.0", + "reactstrap": "9.2.0", "redux": "4.0.5", "redux-thunk": "2.3.0", "string-strip-html": "^8.5.0" @@ -2590,18 +2590,6 @@ "version": "1.2.1", "license": "BSD-3-Clause" }, - "node_modules/@hypnosphi/create-react-context": { - "version": "0.3.1", - "license": "MIT", - "dependencies": { - "gud": "^1.0.0", - "warning": "^4.0.3" - }, - "peerDependencies": { - "prop-types": "^15.0.0", - "react": ">=0.14.0" - } - }, "node_modules/@istanbuljs/load-nyc-config": { "version": "1.1.0", "license": "ISC", @@ -6925,21 +6913,6 @@ "version": "0.7.0", "license": "MIT" }, - "node_modules/deep-equal": { - "version": "1.1.1", - "license": "MIT", - "dependencies": { - "is-arguments": "^1.0.4", - "is-date-object": "^1.0.1", - "is-regex": "^1.0.4", - "object-is": "^1.0.1", - "object-keys": "^1.1.1", - "regexp.prototype.flags": "^1.2.0" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/deep-is": { "version": "0.1.4", "license": "MIT" @@ -9342,10 +9315,6 @@ "version": "1.1.0", "license": "ISC" }, - "node_modules/gud": { - "version": "1.0.0", - "license": "MIT" - }, "node_modules/gzip-size": { "version": "6.0.0", "license": "MIT", @@ -9879,20 +9848,6 @@ "node": ">= 10" } }, - "node_modules/is-arguments": { - "version": "1.1.1", - "license": "MIT", - "dependencies": { - "call-bind": "^1.0.2", - "has-tostringtag": "^1.0.0" - }, - "engines": { - "node": ">= 0.4" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/is-array-buffer": { "version": "3.0.2", "license": "MIT", @@ -12502,32 +12457,21 @@ } }, "node_modules/kpmp-common-components": { - "version": "1.2.3", - "resolved": "https://registry.npmjs.org/kpmp-common-components/-/kpmp-common-components-1.2.3.tgz", - "integrity": "sha512-tdxsKEo3UoE0LJj9WbZVy1CLTzlWyr9XBLQ+2uQjdxvpDuMPW7xSj6oyIle4xbCwvV/zbaLn1sb0UGMXCSZawQ==", + "version": "1.2.7", + "resolved": "https://registry.npmjs.org/kpmp-common-components/-/kpmp-common-components-1.2.7.tgz", + "integrity": "sha512-cqtvuiA5P/9oPTTLyJkPxSy7Mv0hcXDEi/QbPl9mhu2Vz6/f/Xs9/qSgJhTM/HSxtfj6FIN/kIhe+EOYw5YzHw==", "dependencies": { "@fortawesome/fontawesome-free": "6.0.0", "@fortawesome/fontawesome-svg-core": "1.3.0", "@fortawesome/free-brands-svg-icons": "6.0.0", "@fortawesome/free-regular-svg-icons": "6.0.0", "@fortawesome/free-solid-svg-icons": "6.0.0", - "@fortawesome/react-fontawesome": "0.1.7" + "@fortawesome/react-fontawesome": "0.2.0" }, "peerDependencies": { "react": "17.0.2", "react-dom": "17.0.2", - "reactstrap": "8.9.0" - } - }, - "node_modules/kpmp-common-components/node_modules/@fortawesome/react-fontawesome": { - "version": "0.1.7", - "license": "MIT", - "dependencies": { - "prop-types": "^15.5.10" - }, - "peerDependencies": { - "@fortawesome/fontawesome-svg-core": "^1.2.20", - "react": "16.x" + "reactstrap": "9.2.0" } }, "node_modules/kpmp-common-styles": { @@ -13374,20 +13318,6 @@ "url": "https://github.com/sponsors/ljharb" } }, - "node_modules/object-is": { - "version": "1.1.5", - "license": "MIT", - "dependencies": { - "call-bind": "^1.0.2", - "define-properties": "^1.1.3" - }, - "engines": { - "node": ">= 0.4" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/object-keys": { "version": "1.1.1", "license": "MIT", @@ -15584,10 +15514,6 @@ "version": "17.0.2", "license": "MIT" }, - "node_modules/react-lifecycles-compat": { - "version": "3.0.4", - "license": "MIT" - }, "node_modules/react-plotly.js": { "version": "2.6.0", "license": "MIT", @@ -15843,63 +15769,20 @@ } }, "node_modules/reactstrap": { - "version": "8.9.0", - "license": "MIT", + "version": "9.2.0", + "resolved": "https://registry.npmjs.org/reactstrap/-/reactstrap-9.2.0.tgz", + "integrity": "sha512-WWLTEG00qYav0E55PorWHReYTkz5IqkVmQNy0h6U81yqjSp9fOLFGV5pYSVeAUz+yRhU/RTE0oAWy22zr6sOIw==", "dependencies": { "@babel/runtime": "^7.12.5", + "@popperjs/core": "^2.6.0", "classnames": "^2.2.3", "prop-types": "^15.5.8", - "react-popper": "^1.3.6", - "react-transition-group": "^2.3.1" + "react-popper": "^2.2.4", + "react-transition-group": "^4.4.2" }, "peerDependencies": { - "react": ">=16.3.0", - "react-dom": ">=16.3.0" - } - }, - "node_modules/reactstrap/node_modules/dom-helpers": { - "version": "3.4.0", - "license": "MIT", - "dependencies": { - "@babel/runtime": "^7.1.2" - } - }, - "node_modules/reactstrap/node_modules/popper.js": { - "version": "1.16.1", - "license": "MIT", - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/popperjs" - } - }, - "node_modules/reactstrap/node_modules/react-popper": { - "version": "1.3.11", - "license": "MIT", - "dependencies": { - "@babel/runtime": "^7.1.2", - "@hypnosphi/create-react-context": "^0.3.1", - "deep-equal": "^1.1.1", - "popper.js": "^1.14.4", - "prop-types": "^15.6.1", - "typed-styles": "^0.0.7", - "warning": "^4.0.2" - }, - "peerDependencies": { - "react": "0.14.x || ^15.0.0 || ^16.0.0 || ^17.0.0" - } - }, - "node_modules/reactstrap/node_modules/react-transition-group": { - "version": "2.9.0", - "license": "BSD-3-Clause", - "dependencies": { - "dom-helpers": "^3.4.0", - "loose-envify": "^1.4.0", - "prop-types": "^15.6.2", - "react-lifecycles-compat": "^3.0.4" - }, - "peerDependencies": { - "react": ">=15.0.0", - "react-dom": ">=15.0.0" + "react": ">=16.8.0", + "react-dom": ">=16.8.0" } }, "node_modules/read-cache": { @@ -17988,10 +17871,6 @@ "url": "https://github.com/sponsors/ljharb" } }, - "node_modules/typed-styles": { - "version": "0.0.7", - "license": "MIT" - }, "node_modules/typedarray": { "version": "0.0.6", "license": "MIT" diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index d7c63fa9..5f84b2d2 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -54,7 +54,7 @@ class RegionalProteomics extends Component { mapPlotData = (result) => { let plots = {}; let accessionNums = []; - for (let {accession, rpExpressionByTissueType} in result) { + for (let {accession, rpExpressionByTissueType} of result) { plots[accession] = rpExpressionByTissueType; accessionNums.push(accession); } @@ -64,8 +64,8 @@ class RegionalProteomics extends Component { getTabGroup = (accessionNums) => { let tabs = [] - for (let accession in accessionNums) { - tabs.push() + for (let accession of accessionNums) { + tabs.push() } return( {tabs} From dc709dbc3de393a2c0399e46690010e39538a596 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Tue, 5 Dec 2023 15:50:13 -0500 Subject: [PATCH 09/25] KPMP-4434: blank plot --- src/components/DataViz/RegionalProteomics.js | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 5f84b2d2..9d6bbb80 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -14,7 +14,7 @@ import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) { super(props); - this.state = { rpAllData: [] , plotData: {}, accessionNums: [], selectedAccession: ""}; + this.state = { rpAllData: [] , plotData: [], accessionNums: [], selectedAccession: ""}; const queryParam = queryString.parse(props.location.search); if (!this.props.tissueType) { this.props.setTissueType('all') @@ -44,7 +44,7 @@ class RegionalProteomics extends Component { getRPData = () => { fetchRegionalProteomics(this.props.gene.symbol).then((result) => { this.setState({ rpAllData: result }); - this.setState({ selectedAccession: result[0].accession}); + this.setState({ selectedAccession: result[0]["accession"]}); this.mapPlotData(result); // this.setState({ rpTableData: result[this.props.tissueType] }); } @@ -59,7 +59,7 @@ class RegionalProteomics extends Component { accessionNums.push(accession); } this.setState({ plotData: plots }); - this.setState({ accessionNums: accessionNums}) + this.setState({ accessionNums: accessionNums }) } getTabGroup = (accessionNums) => { @@ -73,10 +73,9 @@ class RegionalProteomics extends Component { } render() { - //let plot = this.state.plotData[this.state.selectedAccession]; - //let table = {}; // table = ; - let plot = + let accessionPLot = this.state.plotData?this.state.plotData[this.state.selectedAccession]:[] + let plot = let tabs = this.getTabGroup(this.state.accessionNums); return (
From 8871157317ad3bd3f966e1634fac9ca4e002df2d Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Tue, 5 Dec 2023 16:00:43 -0500 Subject: [PATCH 10/25] KPMP-4435: plot data --- src/components/DataViz/RegionalProteomics.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 9d6bbb80..0a6ff21c 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -14,7 +14,7 @@ import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) { super(props); - this.state = { rpAllData: [] , plotData: [], accessionNums: [], selectedAccession: ""}; + this.state = { rpAllData: [] , plotData: {}, accessionNums: [], selectedAccession: ""}; const queryParam = queryString.parse(props.location.search); if (!this.props.tissueType) { this.props.setTissueType('all') @@ -74,8 +74,8 @@ class RegionalProteomics extends Component { render() { // table = ; - let accessionPLot = this.state.plotData?this.state.plotData[this.state.selectedAccession]:[] - let plot = + let accessionPlot = this.state.plotData?this.state.plotData[this.state.selectedAccession]:{} + let plot = let tabs = this.getTabGroup(this.state.accessionNums); return (
From 625793d750cec135f6847e1d0c149fa85a9a2180 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 11:28:32 -0500 Subject: [PATCH 11/25] KPMP-4435: RP table data --- src/components/DataViz/RegionalProteomics.js | 13 +++++++--- .../RegionalProteomicsTable.js | 25 +++++++++++++++---- 2 files changed, 29 insertions(+), 9 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 0a6ff21c..1259d135 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -73,9 +73,14 @@ class RegionalProteomics extends Component { } render() { - // table = ; - let accessionPlot = this.state.plotData?this.state.plotData[this.state.selectedAccession]:{} - let plot = + let accessionPlotData = {}; + let accessionTableData = []; + if (Object.keys(this.state.plotData).length > 0) { + accessionPlotData = this.state.plotData[this.state.selectedAccession]; + accessionTableData = this.state.plotData[this.state.selectedAccession][this.props.tissueType]; + } + let plot = + let table = let tabs = this.getTabGroup(this.state.accessionNums); return (
@@ -138,7 +143,7 @@ class RegionalProteomics extends Component { - {"table goes here"} + {table} } diff --git a/src/components/ExpressionTables/RegionalProteomicsTable.js b/src/components/ExpressionTables/RegionalProteomicsTable.js index f8ad34c4..e0cf4152 100644 --- a/src/components/ExpressionTables/RegionalProteomicsTable.js +++ b/src/components/ExpressionTables/RegionalProteomicsTable.js @@ -1,5 +1,6 @@ import React, {Component} from "react"; + import { AgGridColumn, AgGridReact } from 'ag-grid-react'; import {Col} from "reactstrap"; import 'ag-grid-community/dist/styles/ag-grid.css'; @@ -11,8 +12,10 @@ import { formatNumberToPrecision } from "../../helpers/Utils"; import {FontAwesomeIcon} from "@fortawesome/react-fontawesome"; import {faInfoCircle} from "@fortawesome/free-solid-svg-icons"; + class CustomHeader extends Component { + render() { return ( @@ -25,29 +28,36 @@ class CustomHeader extends Component { } } + class CustomTooltip extends Component { + getReactContainerClasses() { return ['custom-tooltip']; } + render() { let isHeader = this.props.rowIndex === undefined; return ( - {isHeader &&
{this.props.tooltipText}
} + {isHeader &&
{this.props.tooltipText}
} ) } + } + class RegionalProteomicsTable extends Component { + numberFormatter = (params) => { return formatNumberToPrecision(params.value, 3) }; + render() { return ( @@ -59,10 +69,13 @@ class RegionalProteomicsTable extends Component { frameworkComponents={{customTooltip: CustomTooltip}} tooltipShowDelay={0} > - - + + + + + - +
@@ -84,6 +97,8 @@ class RegionalProteomicsTable extends Component { ) } + } + export default RegionalProteomicsTable; \ No newline at end of file From a099781e22d71411531b3c64463b65dd0786ce0b Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 11:49:09 -0500 Subject: [PATCH 12/25] KPMP-4435: col widths --- .../ExpressionTables/RegionalProteomicsTable.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/components/ExpressionTables/RegionalProteomicsTable.js b/src/components/ExpressionTables/RegionalProteomicsTable.js index e0cf4152..fb1a9a13 100644 --- a/src/components/ExpressionTables/RegionalProteomicsTable.js +++ b/src/components/ExpressionTables/RegionalProteomicsTable.js @@ -69,12 +69,12 @@ class RegionalProteomicsTable extends Component { frameworkComponents={{customTooltip: CustomTooltip}} tooltipShowDelay={0} > - - - - - - + + + + + + Date: Wed, 6 Dec 2023 11:56:18 -0500 Subject: [PATCH 13/25] KPMP-4435: col widths --- .../ExpressionTables/RegionalProteomicsTable.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/components/ExpressionTables/RegionalProteomicsTable.js b/src/components/ExpressionTables/RegionalProteomicsTable.js index fb1a9a13..dcb06f55 100644 --- a/src/components/ExpressionTables/RegionalProteomicsTable.js +++ b/src/components/ExpressionTables/RegionalProteomicsTable.js @@ -69,12 +69,12 @@ class RegionalProteomicsTable extends Component { frameworkComponents={{customTooltip: CustomTooltip}} tooltipShowDelay={0} > - - - - - - + + + + + + Date: Wed, 6 Dec 2023 12:59:16 -0500 Subject: [PATCH 14/25] KPMP-4435: Remove on update action --- src/components/DataViz/RegionalProteomics.js | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 1259d135..94af804a 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -33,9 +33,6 @@ class RegionalProteomics extends Component { }; componentDidUpdate(prevProps, prevState, snapShot) { - if (this.props.tissueType !== prevProps.tissueType) { - this.setState({ rpAllTableData: this.state.rpAllPlotData[this.props.tissueType] }); - } if (this.props.gene !== prevProps.gene) { this.getRPData(); } From b1e0f287732e10401b7d5f65aaab849f5290bb28 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:10:29 -0500 Subject: [PATCH 15/25] KPMP-4435: Gene search issue --- src/components/DataViz/RegionalProteomics.js | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 94af804a..9f298b95 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -7,14 +7,14 @@ import queryString from 'query-string'; import {fetchRegionalProteomics} from "../../helpers/ApolloClient"; import LMDDotPlot from "../Plots/LMDDotPlot"; import RegionalProteomicsTable from "../ExpressionTables/RegionalProteomicsTable"; -import {convertRPResultsToMap, formatTissueType} from "../../helpers/Utils"; +import {formatTissueType} from "../../helpers/Utils"; import {CSVLink} from "react-csv"; import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) { super(props); - this.state = { rpAllData: [] , plotData: {}, accessionNums: [], selectedAccession: ""}; + this.state = { plotData: {}, accessionNums: [], selectedAccession: ""}; const queryParam = queryString.parse(props.location.search); if (!this.props.tissueType) { this.props.setTissueType('all') @@ -40,10 +40,8 @@ class RegionalProteomics extends Component { getRPData = () => { fetchRegionalProteomics(this.props.gene.symbol).then((result) => { - this.setState({ rpAllData: result }); this.setState({ selectedAccession: result[0]["accession"]}); this.mapPlotData(result); - // this.setState({ rpTableData: result[this.props.tissueType] }); } ); }; @@ -76,6 +74,9 @@ class RegionalProteomics extends Component { accessionPlotData = this.state.plotData[this.state.selectedAccession]; accessionTableData = this.state.plotData[this.state.selectedAccession][this.props.tissueType]; } + if (Object.keys(accessionPlotData).length > 0) { + accessionTableData = accessionPlotData[this.props.tissueType]; + } let plot = let table = let tabs = this.getTabGroup(this.state.accessionNums); @@ -107,7 +108,7 @@ class RegionalProteomics extends Component { - Display by: + Protein accession: {tabs} From 54c1e32c2e6626e16bb52197b66b5429f239c191 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:25:13 -0500 Subject: [PATCH 16/25] KPMP-4435: rearrange data --- src/components/DataViz/RegionalProteomics.js | 25 ++++++++++---------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 9f298b95..7f032672 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -14,7 +14,7 @@ import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) { super(props); - this.state = { plotData: {}, accessionNums: [], selectedAccession: ""}; + this.state = { allData: {}, accessionNums: [], selectedAccession: "", tableData: [], plotData: {}}; const queryParam = queryString.parse(props.location.search); if (!this.props.tissueType) { this.props.setTissueType('all') @@ -36,6 +36,9 @@ class RegionalProteomics extends Component { if (this.props.gene !== prevProps.gene) { this.getRPData(); } + if (this.props.tissueType !== prevProps.tissueType) { + this.setState({ tableData: this.state.plotData[this.props.tissueType] }); + } }; getRPData = () => { @@ -47,14 +50,17 @@ class RegionalProteomics extends Component { }; mapPlotData = (result) => { - let plots = {}; + let allData = {}; let accessionNums = []; for (let {accession, rpExpressionByTissueType} of result) { - plots[accession] = rpExpressionByTissueType; + allData[accession] = rpExpressionByTissueType; accessionNums.push(accession); } - this.setState({ plotData: plots }); + this.setState({ allData: allData }); this.setState({ accessionNums: accessionNums }) + let plotData = allData[this.state.selectedAccession]; + this.setState({ plotData: plotData}) + this.setState({ tableData: plotData[this.props.tissueType]}) } getTabGroup = (accessionNums) => { @@ -69,16 +75,11 @@ class RegionalProteomics extends Component { render() { let accessionPlotData = {}; - let accessionTableData = []; - if (Object.keys(this.state.plotData).length > 0) { - accessionPlotData = this.state.plotData[this.state.selectedAccession]; - accessionTableData = this.state.plotData[this.state.selectedAccession][this.props.tissueType]; - } - if (Object.keys(accessionPlotData).length > 0) { - accessionTableData = accessionPlotData[this.props.tissueType]; + if (Object.keys(this.state.allData).length > 0) { + accessionPlotData = this.state.allData[this.state.selectedAccession]; } let plot = - let table = + let table = let tabs = this.getTabGroup(this.state.accessionNums); return (
From 77130f9a90cc6c399ebdecb83985bdc6d3dd1948 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:39:13 -0500 Subject: [PATCH 17/25] KPMP-4435: rearrange data v2 --- src/components/DataViz/RegionalProteomics.js | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 7f032672..c296f25b 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -63,10 +63,16 @@ class RegionalProteomics extends Component { this.setState({ tableData: plotData[this.props.tissueType]}) } + handleAccessionChange = (accession) => { + this.setState({ selectedAccession: accession }) + this.setState({ plotData: this.state.allData[accession]}) + this.setState({ tableData: this.state.allData[accession][this.props.tissueType]}) + } + getTabGroup = (accessionNums) => { let tabs = [] for (let accession of accessionNums) { - tabs.push() + tabs.push() } return( {tabs} @@ -77,6 +83,7 @@ class RegionalProteomics extends Component { let accessionPlotData = {}; if (Object.keys(this.state.allData).length > 0) { accessionPlotData = this.state.allData[this.state.selectedAccession]; + } let plot = let table = From d169e274f139106279f7003c6bb81d797904de5f Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:42:24 -0500 Subject: [PATCH 18/25] KPMP-4435: use stgate --- src/components/DataViz/RegionalProteomics.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index c296f25b..db8ae962 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -80,12 +80,12 @@ class RegionalProteomics extends Component { } render() { - let accessionPlotData = {}; - if (Object.keys(this.state.allData).length > 0) { - accessionPlotData = this.state.allData[this.state.selectedAccession]; - - } - let plot = + // let accessionPlotData = {}; + // if (Object.keys(this.state.allData).length > 0) { + // accessionPlotData = this.state.allData[this.state.selectedAccession]; + // + // } + let plot = let table = let tabs = this.getTabGroup(this.state.accessionNums); return ( From 3b1add5718b7d2c1e33962fadc744ea777f5666c Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:48:53 -0500 Subject: [PATCH 19/25] KPMP-4435: use check obj --- src/components/DataViz/RegionalProteomics.js | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index db8ae962..3531c969 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -80,12 +80,11 @@ class RegionalProteomics extends Component { } render() { - // let accessionPlotData = {}; - // if (Object.keys(this.state.allData).length > 0) { - // accessionPlotData = this.state.allData[this.state.selectedAccession]; - // - // } - let plot = + let accessionPlotData = {}; + if (Object.keys(this.state.plotData).length > 0) { + accessionPlotData = this.state.plotData; + } + let plot = let table = let tabs = this.getTabGroup(this.state.accessionNums); return ( From 12b6f8974effbd3cbe406d2430092460bc09d97e Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 14:56:13 -0500 Subject: [PATCH 20/25] KPMP-4435: use check obj --- src/components/DataViz/RegionalProteomics.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 3531c969..2e81f77c 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -81,7 +81,7 @@ class RegionalProteomics extends Component { render() { let accessionPlotData = {}; - if (Object.keys(this.state.plotData).length > 0) { + if (this.state.plotData && Object.keys(this.state.plotData).length > 0) { accessionPlotData = this.state.plotData; } let plot = From a4ed95d752931be027af21e7d27bd56584a7874f Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 15:02:32 -0500 Subject: [PATCH 21/25] KPMP-4435: don't pass obj --- src/components/DataViz/RegionalProteomics.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 2e81f77c..ebd33f3a 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -72,7 +72,7 @@ class RegionalProteomics extends Component { getTabGroup = (accessionNums) => { let tabs = [] for (let accession of accessionNums) { - tabs.push() + tabs.push() } return( {tabs} From 312d734bb7da3b34f6834cc994dab9d1bca6065e Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 15:03:13 -0500 Subject: [PATCH 22/25] KPMP-4435: don't pass obj --- src/components/DataViz/RegionalProteomics.js | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index ebd33f3a..3b51a3e1 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -80,11 +80,11 @@ class RegionalProteomics extends Component { } render() { - let accessionPlotData = {}; - if (this.state.plotData && Object.keys(this.state.plotData).length > 0) { - accessionPlotData = this.state.plotData; - } - let plot = + // let accessionPlotData = {}; + // if (this.state.plotData && Object.keys(this.state.plotData).length > 0) { + // accessionPlotData = this.state.plotData; + // } + let plot = let table = let tabs = this.getTabGroup(this.state.accessionNums); return ( From 84b1411a94484d9c695393958320cdcadf6ab8e2 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 15:15:36 -0500 Subject: [PATCH 23/25] KPMP-4435: simplify --- src/components/DataViz/RegionalProteomics.js | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 3b51a3e1..5368f583 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -58,8 +58,7 @@ class RegionalProteomics extends Component { } this.setState({ allData: allData }); this.setState({ accessionNums: accessionNums }) - let plotData = allData[this.state.selectedAccession]; - this.setState({ plotData: plotData}) + this.setState({ plotData: allData[this.state.selectedAccession]}) this.setState({ tableData: plotData[this.props.tissueType]}) } @@ -80,10 +79,6 @@ class RegionalProteomics extends Component { } render() { - // let accessionPlotData = {}; - // if (this.state.plotData && Object.keys(this.state.plotData).length > 0) { - // accessionPlotData = this.state.plotData; - // } let plot = let table = let tabs = this.getTabGroup(this.state.accessionNums); From 1784e508ff860daae6a950ad0b489ea2b0db43d9 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 15:18:10 -0500 Subject: [PATCH 24/25] KPMP-4435: switch it back --- src/components/DataViz/RegionalProteomics.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 5368f583..2827d1de 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -58,7 +58,8 @@ class RegionalProteomics extends Component { } this.setState({ allData: allData }); this.setState({ accessionNums: accessionNums }) - this.setState({ plotData: allData[this.state.selectedAccession]}) + let plotData = allData[this.state.selectedAccession]; + this.setState({ plotData: plotData}) this.setState({ tableData: plotData[this.props.tissueType]}) } From 0b3b5ebbdf0a56a29434e6249923a3ee539e4b39 Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Wed, 6 Dec 2023 15:45:21 -0500 Subject: [PATCH 25/25] KPMP-4435: unused imports --- src/components/DataViz/RegionalProteomics.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/components/DataViz/RegionalProteomics.js b/src/components/DataViz/RegionalProteomics.js index 2827d1de..6fa36ca6 100644 --- a/src/components/DataViz/RegionalProteomics.js +++ b/src/components/DataViz/RegionalProteomics.js @@ -2,14 +2,12 @@ import React, { Component } from 'react'; import {Container, Row, Col, ButtonGroup, Button} from 'reactstrap'; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import DataTypeSelectorContainer from './DataTypeSelectorContainer'; -import {faDownload, faShare} from "@fortawesome/free-solid-svg-icons"; +import {faShare} from "@fortawesome/free-solid-svg-icons"; import queryString from 'query-string'; import {fetchRegionalProteomics} from "../../helpers/ApolloClient"; import LMDDotPlot from "../Plots/LMDDotPlot"; import RegionalProteomicsTable from "../ExpressionTables/RegionalProteomicsTable"; import {formatTissueType} from "../../helpers/Utils"; -import {CSVLink} from "react-csv"; -import {handleGoogleAnalyticsEvent} from "../../helpers/googleAnalyticsHelper"; class RegionalProteomics extends Component { constructor(props) {