From 5b86df92d55dc2ba2d7cd5ec6b87a0ee1d63ce8d Mon Sep 17 00:00:00 2001 From: afonso Date: Fri, 31 May 2024 15:17:04 +0100 Subject: [PATCH 1/3] ESCKAN fix: Move phenotype colormap to context --- package.json | 2 + src/components/Connections.tsx | 375 ++++--- src/components/SummaryFiltersDropdown.tsx | 12 +- src/components/common/Heatmap.tsx | 27 +- src/components/common/Types.ts | 6 +- .../connections/PhenotypeLegend.tsx | 116 +- src/context/DataContext.ts | 6 +- src/context/DataContextProvider.tsx | 25 +- src/services/summaryHeatmapService.ts | 317 +++--- yarn.lock | 994 ++++++++---------- 10 files changed, 876 insertions(+), 1004 deletions(-) diff --git a/package.json b/package.json index 0504445..6932784 100644 --- a/package.json +++ b/package.json @@ -20,6 +20,7 @@ "@mui/material": "^5.15.9", "@projectstorm/react-canvas-core": "^7.0.2", "@projectstorm/react-diagrams": "^7.0.3", + "chroma-js": "^2.4.2", "react": "^18.2.0", "react-dom": "^18.2.0", "react-heatmap-grid": "^0.9.0", @@ -27,6 +28,7 @@ "react-router-dom": "^6.22.2" }, "devDependencies": { + "@types/chroma-js": "^2.4.4", "@types/react": "^18.2.55", "@types/react-dom": "^18.2.19", "@typescript-eslint/eslint-plugin": "^6.21.0", diff --git a/src/components/Connections.tsx b/src/components/Connections.tsx index a8d74d2..9bdb702 100644 --- a/src/components/Connections.tsx +++ b/src/components/Connections.tsx @@ -1,218 +1,209 @@ -import React, { useEffect, useMemo, useState } from "react"; -import { Box, Chip, TextField, Typography } from "@mui/material"; -import { ArrowRightIcon } from "./icons"; -import { vars } from "../theme/variables"; -import { HierarchicalItem, PhenotypeKsIdMap, SummaryType, KsMapType, PhenotypeType } from "./common/Types"; -import { useDataContext } from "../context/DataContext.ts"; +import React, {useEffect, useMemo, useState} from "react"; +import {Box, Chip, TextField, Typography} from "@mui/material"; +import {ArrowRightIcon} from "./icons"; +import {vars} from "../theme/variables"; +import {HierarchicalItem, PhenotypeKsIdMap, SummaryType, KsMapType} from "./common/Types"; +import {useDataContext} from "../context/DataContext.ts"; import { - calculateSecondaryConnections, - convertViaToString, generatePhenotypeColors, - getAllPhenotypes, getAllViasFromConnections, getDestinations, getNerveFilters, - getSecondaryHeatmapData, - getXAxisForHeatmap, + calculateSecondaryConnections, + convertViaToString, + getAllPhenotypes, getAllViasFromConnections, getDestinations, getNerveFilters, + getSecondaryHeatmapData, + getXAxisForHeatmap, } from "../services/summaryHeatmapService.ts"; -import { getYAxis, getKnowledgeStatementMap } from "../services/heatmapService.ts"; +import {getYAxis, getKnowledgeStatementMap} from "../services/heatmapService.ts"; import SummaryHeader from "./connections/SummaryHeader"; import SummaryInstructions from "./connections/SummaryInstructions.tsx"; import PhenotypeLegend from "./connections/PhenotypeLegend.tsx"; import HeatmapGrid from "./common/Heatmap.tsx"; -import { Organ } from "../models/explorer.ts"; +import {Organ} from "../models/explorer.ts"; import SummaryDetails from "./connections/SummaryDetails.tsx"; import SummaryFiltersDropdown from "./SummaryFiltersDropdown.tsx"; -const { gray700, gray600A, gray100 } = vars; +const {gray700, gray600A, gray100} = vars; const styles = { - heading: { - fontSize: '0.875rem', - fontWeight: '500', - lineHeight: '1.25rem', - color: gray700, - marginBottom: '0.5rem' - }, - text: { - fontSize: '0.875rem', - fontWeight: 400, - lineHeight: '1.25rem', - color: gray600A - } + heading: { + fontSize: '0.875rem', + fontWeight: '500', + lineHeight: '1.25rem', + color: gray700, + marginBottom: '0.5rem' + }, + text: { + fontSize: '0.875rem', + fontWeight: 400, + lineHeight: '1.25rem', + color: gray600A + } } function Connections() { - const [showConnectionDetails, setShowConnectionDetails] = useState(SummaryType.Instruction); - const [connectionsMap, setConnectionsMap] = useState>(new Map()); - const [connectionPage, setConnectionPage] = useState(1); // represents the page number / index of the connections - if (x,y) has 4 connections, then connectionPage will be 1, 2, 3, 4 - const [yAxis, setYAxis] = useState([]); - const [selectedCell, setSelectedCell] = useState<{ x: number, y: number } | null>(null); // useful for coordinates - const [phenotypes, setPhenotypes] = useState({}); - const [knowledgeStatementsMap, setKnowledgeStatementsMap] = useState({}); - const [xAxis, setXAxis] = useState([]); - - const { selectedConnectionSummary, majorNerves, hierarchicalNodes, knowledgeStatements, summaryFilters } = useDataContext(); - - useEffect(() => { - // By default on the first render, show the instruction/summary - if (selectedConnectionSummary) { - setShowConnectionDetails(SummaryType.Summary); - } - }, [selectedConnectionSummary]) - - // Values from the selected connection - In the SummaryType.summary - const viasConnection = getAllViasFromConnections(selectedConnectionSummary?.connections || {} as KsMapType); - const viasStatement = convertViaToString(Object.values(viasConnection)) - const totalConnectionCount = Object.keys(selectedConnectionSummary?.connections || {} as KsMapType).length; - const phenotypeNamesArray = useMemo(() => getAllPhenotypes(selectedConnectionSummary?.connections || {} as KsMapType), [selectedConnectionSummary]); - - - useEffect(() => { - // Generate the phenotype colors and set the phenotypes - if (selectedConnectionSummary && phenotypeNamesArray && phenotypeNamesArray.length > 0) { - const phenotypeColors: string[] = generatePhenotypeColors(phenotypeNamesArray.length) - const phenotypes: PhenotypeType = {}; - phenotypeNamesArray.forEach((phenotype, index) => { - phenotypes[phenotype] = { - label: phenotype, - color: phenotypeColors[index], + const [showConnectionDetails, setShowConnectionDetails] = useState(SummaryType.Instruction); + const [connectionsMap, setConnectionsMap] = useState>(new Map()); + const [connectionPage, setConnectionPage] = useState(1); // represents the page number / index of the connections - if (x,y) has 4 connections, then connectionPage will be 1, 2, 3, 4 + const [yAxis, setYAxis] = useState([]); + const [selectedCell, setSelectedCell] = useState<{ x: number, y: number } | null>(null); // useful for coordinates + const [knowledgeStatementsMap, setKnowledgeStatementsMap] = useState({}); + const [xAxis, setXAxis] = useState([]); + + const { + selectedConnectionSummary, + majorNerves, + hierarchicalNodes, + knowledgeStatements, + summaryFilters + } = useDataContext(); + + useEffect(() => { + // By default on the first render, show the instruction/summary + if (selectedConnectionSummary) { + setShowConnectionDetails(SummaryType.Summary); } - }) - setPhenotypes(phenotypes); - } - }, [phenotypeNamesArray, selectedConnectionSummary]) + }, [selectedConnectionSummary]) - const nerves = getNerveFilters(viasConnection, majorNerves); + // Values from the selected connection - In the SummaryType.summary + const viasConnection = getAllViasFromConnections(selectedConnectionSummary?.connections || {} as KsMapType); + const viasStatement = convertViaToString(Object.values(viasConnection)) + const totalConnectionCount = Object.keys(selectedConnectionSummary?.connections || {} as KsMapType).length; + const nerves = getNerveFilters(viasConnection, majorNerves); - useEffect(() => { - // calculate the connectionsMap for the secondary heatmap - if (selectedConnectionSummary && phenotypes && selectedConnectionSummary.hierarchy && hierarchicalNodes) { - const destinations = getDestinations(selectedConnectionSummary); - const connections = calculateSecondaryConnections(hierarchicalNodes, destinations, knowledgeStatements, summaryFilters, selectedConnectionSummary.hierarchy) - setConnectionsMap(connections); - } - }, [hierarchicalNodes, selectedConnectionSummary, summaryFilters, knowledgeStatements, phenotypes]); + useEffect(() => { + // calculate the connectionsMap for the secondary heatmap + if (selectedConnectionSummary && selectedConnectionSummary.hierarchy && hierarchicalNodes) { + const destinations = getDestinations(selectedConnectionSummary); + const connections = calculateSecondaryConnections(hierarchicalNodes, destinations, knowledgeStatements, summaryFilters, selectedConnectionSummary.hierarchy) + setConnectionsMap(connections); + } + }, [hierarchicalNodes, selectedConnectionSummary, summaryFilters, knowledgeStatements]); + const selectedPhenotypes = useMemo(() => getAllPhenotypes(connectionsMap), [connectionsMap]); - useEffect(() => { - // set the xAxis for the heatmap - if (selectedConnectionSummary) { - const xAxis = getXAxisForHeatmap(selectedConnectionSummary?.endOrgan || {} as Organ) - setXAxis(xAxis); - } - }, [selectedConnectionSummary]); - - useEffect(() => { - // set the yAxis for the heatmap - if (selectedConnectionSummary && hierarchicalNodes) { - const hierarchyNode = { - [selectedConnectionSummary.hierarchy.id]: selectedConnectionSummary.hierarchy - } - const yHierarchicalItem = getYAxis(hierarchicalNodes, hierarchyNode); - setYAxis(yHierarchicalItem); - } - }, [selectedConnectionSummary, hierarchicalNodes]); - - - const handleCellClick = (x: number, y: number, yId: string): void => { - // when the heatmap cell is clicked - setSelectedCell({ x, y }); - const row = connectionsMap.get(yId); - if (row) { - setConnectionPage(1) - const ksIds = Object.values(row[x]).reduce((acc, phenotypeData) => { - return acc.concat(phenotypeData.ksIds); - }, [] as string[]); - - if (selectedConnectionSummary && Object.keys(selectedConnectionSummary.connections).length !== 0) { - setShowConnectionDetails(SummaryType.DetailedSummary); - const ksMap = getKnowledgeStatementMap(ksIds, knowledgeStatements); - setKnowledgeStatementsMap(ksMap); - } - } - } - - const heatmapData = useMemo(() => { - return getSecondaryHeatmapData(yAxis, connectionsMap); - }, [yAxis, connectionsMap]); - - return ( - - - { - showConnectionDetails === SummaryType.Instruction && ( - - ) - } - - {showConnectionDetails === SummaryType.DetailedSummary ? ( - - ) : showConnectionDetails === SummaryType.Instruction ? (<>) : ( - <> - - - - Connection origin - - - - - End Organ - - - - - - Amount of connections - - - - - Connections are through these nerves - {viasStatement} - - - - - - Summary map - - Summary map shows the connections of the selected connection origin and end organ with phenotypes. Select individual squares to view the details of each connections. - - - - - - - - - ) - } + useEffect(() => { + // set the xAxis for the heatmap + if (selectedConnectionSummary) { + const xAxis = getXAxisForHeatmap(selectedConnectionSummary?.endOrgan || {} as Organ) + setXAxis(xAxis); + } + }, [selectedConnectionSummary]); + + useEffect(() => { + // set the yAxis for the heatmap + if (selectedConnectionSummary && hierarchicalNodes) { + const hierarchyNode = { + [selectedConnectionSummary.hierarchy.id]: selectedConnectionSummary.hierarchy + } + const yHierarchicalItem = getYAxis(hierarchicalNodes, hierarchyNode); + setYAxis(yHierarchicalItem); + } + }, [selectedConnectionSummary, hierarchicalNodes]); + + + const handleCellClick = (x: number, y: number, yId: string): void => { + // when the heatmap cell is clicked + setSelectedCell({x, y}); + const row = connectionsMap.get(yId); + if (row) { + setConnectionPage(1) + const ksIds = Object.values(row[x]).reduce((acc, phenotypeData) => { + return acc.concat(phenotypeData.ksIds); + }, [] as string[]); + + if (selectedConnectionSummary && Object.keys(selectedConnectionSummary.connections).length !== 0) { + setShowConnectionDetails(SummaryType.DetailedSummary); + const ksMap = getKnowledgeStatementMap(ksIds, knowledgeStatements); + setKnowledgeStatementsMap(ksMap); + } + } + } - - ) + const heatmapData = useMemo(() => { + return getSecondaryHeatmapData(yAxis, connectionsMap); + }, [yAxis, connectionsMap]); + + return ( + + + { + showConnectionDetails === SummaryType.Instruction && ( + + ) + } + + {showConnectionDetails === SummaryType.DetailedSummary ? ( + + ) : showConnectionDetails === SummaryType.Instruction ? (<>) : ( + <> + + + + Connection + origin + + + + + End Organ + + + + + + Amount of connections + + + + + Connections are through these nerves + {viasStatement} + + + + + + Summary + map + + Summary map shows the connections of the selected connection origin and end organ with + phenotypes. Select individual squares to view the details of each connections. + + + + + + + + + ) + } + + + + ) } export default Connections diff --git a/src/components/SummaryFiltersDropdown.tsx b/src/components/SummaryFiltersDropdown.tsx index 0acb327..8429d19 100644 --- a/src/components/SummaryFiltersDropdown.tsx +++ b/src/components/SummaryFiltersDropdown.tsx @@ -1,7 +1,7 @@ import { useMemo } from "react"; import { SummaryFilters, useDataContext } from "../context/DataContext"; import CustomFilterDropdown from "./common/CustomFilterDropdown"; -import { Option, PhenotypeType } from "./common/Types"; +import { Option } from "./common/Types"; import { Box } from "@mui/material"; import { searchNerveFilter, searchPhenotypeFilter } from "../services/searchService"; import { OTHER_PHENOTYPE_LABEL } from "../settings"; @@ -27,7 +27,7 @@ const filterConfig: FilterConfig[] = [ const SummaryFiltersDropdown = ({ nerves, phenotypes }: { nerves: { [key: string]: string }, - phenotypes: PhenotypeType + phenotypes: string[] }) => { const { summaryFilters, setSummaryFilters } = useDataContext(); @@ -39,10 +39,10 @@ const SummaryFiltersDropdown = ({ nerves, phenotypes }: { content: [] })); } - const convertPhenotypesToOptions = (phenotypes: PhenotypeType): Option[] => { - return Object.values(phenotypes).map(phenotype => ({ - id: phenotype.label, - label: phenotype.label, + const convertPhenotypesToOptions = (phenotypes: string[]): Option[] => { + return phenotypes.map(phenotype => ({ + id: phenotype, + label: phenotype, group: 'Phenotype', content: [] })).filter(phenotype => phenotype.label !== OTHER_PHENOTYPE_LABEL); diff --git a/src/components/common/Heatmap.tsx b/src/components/common/Heatmap.tsx index c17376a..0101366 100644 --- a/src/components/common/Heatmap.tsx +++ b/src/components/common/Heatmap.tsx @@ -4,10 +4,11 @@ import {vars} from "../../theme/variables"; import CollapsibleList from "./CollapsibleList"; import HeatMap from "react-heatmap-grid"; import HeatmapTooltip, {HeatmapTooltipRow} from "./HeatmapTooltip"; -import {HierarchicalItem, PhenotypeType, PhenotypeKsIdMap} from "./Types.ts"; +import {HierarchicalItem, PhenotypeKsIdMap} from "./Types.ts"; import {getNormalizedValueForMinMax} from "../../services/summaryHeatmapService.ts"; import {generateYLabelsAndIds, getPhenotypeColors} from "../../services/heatmapService.ts"; import {OTHER_PHENOTYPE_LABEL} from "../../settings.ts"; +import {useDataContext} from "../../context/DataContext.ts"; const {gray50, primaryPurple500, gray100A, gray500} = vars; @@ -22,7 +23,6 @@ interface HeatmapGridProps { selectedCell?: { x: number, y: number } | null; heatmapData?: number[][]; secondaryHeatmapData?: PhenotypeKsIdMap[][]; - phenotypes?: PhenotypeType; } const prepareSecondaryHeatmapData = (data?: PhenotypeKsIdMap[][]): number[][] => { @@ -34,10 +34,17 @@ const prepareSecondaryHeatmapData = (data?: PhenotypeKsIdMap[][]): number[][] => const HeatmapGrid: FC = ({ - xAxis, yAxis, setYAxis, - xAxisLabel, yAxisLabel, - onCellClick, selectedCell, heatmapData, secondaryHeatmapData, phenotypes + xAxis, + yAxis, + setYAxis, + xAxisLabel, + yAxisLabel, + onCellClick, + selectedCell, + heatmapData, + secondaryHeatmapData }) => { + const {phenotypesColorMap} = useDataContext() const secondary = !!secondaryHeatmapData; const yAxisData = generateYLabelsAndIds(yAxis); @@ -91,16 +98,16 @@ const HeatmapGrid: FC = ({ _y: number ) => { // Gets the color for secondary heatmap cell based on the phenotypes - if (phenotypes && secondary && secondaryHeatmapData && secondaryHeatmapData[_y] && secondaryHeatmapData[_y][_x]) { + if (secondary && secondaryHeatmapData && secondaryHeatmapData[_y] && secondaryHeatmapData[_y][_x]) { const heatmapCellPhenotypes = secondaryHeatmapData[_y][_x]; const phenotypeColorsSet = new Set(); Object.keys(heatmapCellPhenotypes).forEach(phenotype => { - const phnColor = phenotypes[phenotype]?.color; + const phnColor = phenotypesColorMap[phenotype]?.color; if (phnColor) { phenotypeColorsSet.add(phnColor); } else { - phenotypeColorsSet.add(phenotypes[OTHER_PHENOTYPE_LABEL].color); + phenotypeColorsSet.add(phenotypesColorMap[OTHER_PHENOTYPE_LABEL].color); } }); @@ -112,11 +119,11 @@ const HeatmapGrid: FC = ({ }; const getTooltipRows = (xIndex: number, yIndex: number): HeatmapTooltipRow[] => { - if (secondary && secondaryHeatmapData && phenotypes && secondaryHeatmapData[yIndex] && secondaryHeatmapData[yIndex][xIndex]) { + if (secondary && secondaryHeatmapData && secondaryHeatmapData[yIndex] && secondaryHeatmapData[yIndex][xIndex]) { const heatmapCellPhenotypes = secondaryHeatmapData[yIndex][xIndex]; return Object.keys(heatmapCellPhenotypes).map(phenotype => ({ - color: phenotypes[phenotype]?.color || phenotypes[OTHER_PHENOTYPE_LABEL].color, + color: phenotypesColorMap[phenotype]?.color || phenotypesColorMap[OTHER_PHENOTYPE_LABEL].color, name: phenotype, count: heatmapCellPhenotypes[phenotype].ksIds.length })); diff --git a/src/components/common/Types.ts b/src/components/common/Types.ts index 5c3c72c..55c959a 100644 --- a/src/components/common/Types.ts +++ b/src/components/common/Types.ts @@ -45,8 +45,4 @@ export interface HierarchicalItem { export type PhenotypeDetail = { label: string; color: string; -}; - -export type PhenotypeType = { - [key: string]: PhenotypeDetail; -} \ No newline at end of file +}; \ No newline at end of file diff --git a/src/components/connections/PhenotypeLegend.tsx b/src/components/connections/PhenotypeLegend.tsx index 45e7b3b..32de75e 100644 --- a/src/components/connections/PhenotypeLegend.tsx +++ b/src/components/connections/PhenotypeLegend.tsx @@ -1,67 +1,67 @@ -import { Box, Typography } from "@mui/material" -import { PhenotypeDetail, PhenotypeType } from "../common/Types" -import { vars } from "../../theme/variables"; +import {Box, Typography} from "@mui/material" +import {vars} from "../../theme/variables"; +import {useDataContext} from "../../context/DataContext.ts"; -const { gray100 } = vars; +const {gray100} = vars; const PhenotypeLegend = ( - { phenotypes }: { phenotypes: PhenotypeType } + {phenotypes}: { phenotypes: string[] } ) => { - const phenotypesLegends = Object.values(phenotypes); - return ( - - - Phenotype + const {phenotypesColorMap} = useDataContext() + return ( + + + Phenotype - - {phenotypesLegends?.map((phenotype: PhenotypeDetail) => ( - - - {phenotype.label} - - ))} - - - - ) + + {phenotypes.map((phenotype: string) => ( + + + {phenotype} + + ))} + + + + ) } diff --git a/src/context/DataContext.ts b/src/context/DataContext.ts index 35a7d43..c1d7298 100644 --- a/src/context/DataContext.ts +++ b/src/context/DataContext.ts @@ -1,6 +1,6 @@ import React, {createContext, useContext} from "react"; import {Organ, HierarchicalNode, KnowledgeStatement} from "../models/explorer"; -import {Option} from "../components/common/Types.ts"; +import {Option, PhenotypeDetail} from "../components/common/Types.ts"; import { KsMapType } from "../components/common/Types"; export interface Filters { @@ -37,6 +37,7 @@ export interface DataContext { setSummaryFilters: React.Dispatch>; selectedConnectionSummary: ConnectionSummary | null; setConnectionSummary: React.Dispatch>; + phenotypesColorMap: Record; } export const DataContext = createContext({ @@ -62,7 +63,8 @@ export const DataContext = createContext({ }, selectedConnectionSummary: null, setConnectionSummary: () => { - } + }, + phenotypesColorMap: {} }); export const useDataContext = () => useContext(DataContext); diff --git a/src/context/DataContextProvider.tsx b/src/context/DataContextProvider.tsx index f131304..f984152 100644 --- a/src/context/DataContextProvider.tsx +++ b/src/context/DataContextProvider.tsx @@ -1,6 +1,9 @@ -import {PropsWithChildren, useState} from 'react'; +import {PropsWithChildren, useMemo, useState} from 'react'; import { DataContext, Filters, ConnectionSummary, SummaryFilters } from "./DataContext"; import {HierarchicalNode, KnowledgeStatement, Organ} from "../models/explorer.ts"; +import {PhenotypeDetail} from "../components/common/Types.ts"; +import {generatePhenotypeColors} from "../services/summaryHeatmapService.ts"; +import {OTHER_PHENOTYPE_LABEL} from "../settings.ts"; export const DataContextProvider = ({ @@ -30,6 +33,23 @@ export const DataContextProvider = ({ const [selectedConnectionSummary, setSelectedConnectionSummary] = useState(null); + const phenotypes = useMemo(() => { + const allPhenotypes = Object.values(knowledgeStatements).map(ks => ks.phenotype || OTHER_PHENOTYPE_LABEL); + return Array.from(new Set(allPhenotypes)); // Get unique phenotypes + }, [knowledgeStatements]); + + const phenotypesColorMap = useMemo(() => { + const colors = generatePhenotypeColors(phenotypes.length); + const colorMap: Record = {}; + phenotypes.forEach((phenotype, index) => { + colorMap[phenotype] = { + label: phenotype, + color: colors[index] + }; + }); + return colorMap; + }, [phenotypes]); + const dataContextValue = { filters, @@ -41,7 +61,8 @@ export const DataContextProvider = ({ knowledgeStatements, setFilters, selectedConnectionSummary, - setConnectionSummary: setSelectedConnectionSummary + setConnectionSummary: setSelectedConnectionSummary, + phenotypesColorMap }; return ( diff --git a/src/services/summaryHeatmapService.ts b/src/services/summaryHeatmapService.ts index bf66508..c71890d 100644 --- a/src/services/summaryHeatmapService.ts +++ b/src/services/summaryHeatmapService.ts @@ -1,74 +1,76 @@ -import { HierarchicalItem, PhenotypeKsIdMap, KsMapType } from "../components/common/Types.ts"; -import { ConnectionSummary, SummaryFilters } from "../context/DataContext.ts"; -import { HierarchicalNode, KnowledgeStatement, Organ, BaseEntity } from "../models/explorer.ts"; -import { FIXED_FOUR_PHENOTYPE_COLORS_ARRAY, OTHER_PHENOTYPE_LABEL } from "../settings.ts"; - +import chroma from 'chroma-js'; +import {HierarchicalItem, PhenotypeKsIdMap, KsMapType} from "../components/common/Types.ts"; +import {ConnectionSummary, SummaryFilters} from "../context/DataContext.ts"; +import {HierarchicalNode, KnowledgeStatement, Organ, BaseEntity} from "../models/explorer.ts"; +import {OTHER_PHENOTYPE_LABEL} from "../settings.ts"; export const generatePhenotypeColors = (num: number) => { - const colors: string[] = FIXED_FOUR_PHENOTYPE_COLORS_ARRAY; - for (let i = 4; i < num; i++) { - colors.push(`rgb(${Math.floor(Math.random() * 256)}, ${Math.floor(Math.random() * 256)}, ${Math.floor(Math.random() * 256)})`); - } - return colors; -} + const scale = chroma.scale(['red', 'blue', 'green', 'yellow', 'purple', 'orange', 'brown']).mode('lch').colors(num); + return scale; +}; export function convertViaToString(via: string[]): string { - if (via.length === 0) return '-'; - if (via.length > 1) { - return via.join(', ').replace(/,(?=[^,]*$)/, ' and'); - } - return via[0]; + if (via.length === 0) return '-'; + if (via.length > 1) { + return via.join(', ').replace(/,(?=[^,]*$)/, ' and'); + } + return via[0]; } export function getAllViasFromConnections(connections: KsMapType): { [key: string]: string } { - const vias: { [key: string]: string } = {}; - Object.values(connections).forEach(connection => { - if (connection.vias && connection.vias.length > 0) { - const flattenedVias = connection.vias.flatMap(via => via.anatomical_entities); - flattenedVias.forEach(via => { - vias[via.id] = via.name; - }); - } - }); - return vias; + const vias: { [key: string]: string } = {}; + Object.values(connections).forEach(connection => { + if (connection.vias && connection.vias.length > 0) { + const flattenedVias = connection.vias.flatMap(via => via.anatomical_entities); + flattenedVias.forEach(via => { + vias[via.id] = via.name; + }); + } + }); + return vias; } -export function getAllPhenotypes(connections: KsMapType): string[] { - const phenotypeNames: Set = new Set(); - Object.values(connections)?.forEach(connection => { - if (connection?.phenotype) { - phenotypeNames.add(connection.phenotype); - } else { - phenotypeNames.add(OTHER_PHENOTYPE_LABEL); - } - }); - return Array.from(phenotypeNames) +export function getAllPhenotypes(connections: Map): string[] { + const phenotypeNames: Set = new Set(); + + connections.forEach(phenotypeKsIdMaps => { + phenotypeKsIdMaps.forEach(phenotypeKsIdMap => { + Object.keys(phenotypeKsIdMap).forEach(phenotype => { + if (phenotype) { + phenotypeNames.add(phenotype); + } else { + phenotypeNames.add(OTHER_PHENOTYPE_LABEL); + } + }); + }); + }); + + return Array.from(phenotypeNames); } export const getNerveFilters = (viasConnection: { [key: string]: string }, majorNerves: Set) => { - const nerves: { [key: string]: string } = {}; - Object.keys(viasConnection).forEach(via => { - if (majorNerves.has(via)) { - nerves[via] = viasConnection[via]; - } - }); - return nerves; + const nerves: { [key: string]: string } = {}; + Object.keys(viasConnection).forEach(via => { + if (majorNerves.has(via)) { + nerves[via] = viasConnection[via]; + } + }); + return nerves; } - export function summaryFilterKnowledgeStatements(knowledgeStatements: Record, summaryFilters: SummaryFilters): Record { - const phenotypeIds = summaryFilters.Phenotype.map(option => option.id); - const nerveIds = summaryFilters.Nerve.map(option => option.id); - return Object.entries(knowledgeStatements).reduce((filtered, [id, ks]) => { - const phenotypeMatch = !phenotypeIds.length || phenotypeIds.includes(ks.phenotype); - const nerveMatch = !nerveIds.length || ks.vias?.some(via => via.anatomical_entities.map(entity => entity.id).some(id => nerveIds.includes(id))); - if (phenotypeMatch && nerveMatch) { - filtered[id] = ks; - } - return filtered; - }, {} as Record); + const phenotypeIds = summaryFilters.Phenotype.map(option => option.id); + const nerveIds = summaryFilters.Nerve.map(option => option.id); + return Object.entries(knowledgeStatements).reduce((filtered, [id, ks]) => { + const phenotypeMatch = !phenotypeIds.length || phenotypeIds.includes(ks.phenotype); + const nerveMatch = !nerveIds.length || ks.vias?.some(via => via.anatomical_entities.map(entity => entity.id).some(id => nerveIds.includes(id))); + if (phenotypeMatch && nerveMatch) { + filtered[id] = ks; + } + return filtered; + }, {} as Record); } @@ -79,35 +81,35 @@ export function summaryFilterKnowledgeStatements(knowledgeStatements: Record) { - const newData: PhenotypeKsIdMap[][] = []; - - function addDataForItem(item: HierarchicalItem) { - const itemData = connections.get(item.id); - if (itemData) { - newData.push(itemData); - } - } - - function traverseItems(items: HierarchicalItem[], fetchNextLevel: boolean) { - items?.forEach(item => { - if (item.expanded) { - // Fetch data for the current expanded item - addDataForItem(item); - // Traverse further into the expanded item - if (item.children && typeof item.children[0] !== 'string') { - traverseItems(item.children as HierarchicalItem[], true); - } - } else if (fetchNextLevel) { - // Fetch data for the immediate children of the last expanded item - addDataForItem(item); - } - }); - } - - // Start traversal with the initial yAxis, allowing to fetch immediate children of the root if expanded - traverseItems(yAxis, true); - - return newData; + const newData: PhenotypeKsIdMap[][] = []; + + function addDataForItem(item: HierarchicalItem) { + const itemData = connections.get(item.id); + if (itemData) { + newData.push(itemData); + } + } + + function traverseItems(items: HierarchicalItem[], fetchNextLevel: boolean) { + items?.forEach(item => { + if (item.expanded) { + // Fetch data for the current expanded item + addDataForItem(item); + // Traverse further into the expanded item + if (item.children && typeof item.children[0] !== 'string') { + traverseItems(item.children as HierarchicalItem[], true); + } + } else if (fetchNextLevel) { + // Fetch data for the immediate children of the last expanded item + addDataForItem(item); + } + }); + } + + // Start traversal with the initial yAxis, allowing to fetch immediate children of the root if expanded + traverseItems(yAxis, true); + + return newData; } @@ -118,93 +120,94 @@ export function getSecondaryHeatmapData(yAxis: HierarchicalItem[], connections: // If node.destinationDetails is present, store the phenotypes and knowledge statement ids for each end organ in the result array // If node.children is present, recursively call the function on each child node and merge the results export function calculateSecondaryConnections( - hierarchicalNodes: Record, endorgans: Record, - allKnowledgeStatements: Record, summaryFilters: SummaryFilters, - hierarchyNode: HierarchicalNode + hierarchicalNodes: Record, endorgans: Record, + allKnowledgeStatements: Record, summaryFilters: SummaryFilters, + hierarchyNode: HierarchicalNode ): Map { - // Apply filters to organs and knowledge statements - const knowledgeStatements = summaryFilterKnowledgeStatements(allKnowledgeStatements, summaryFilters); - - const organIndexMap = Object.values(endorgans).reduce>((map, organ, index) => { - map[organ.id] = index; - return map; - }, {}); - - // Memoization map to store computed results for nodes - const memo = new Map(); - - // Function to compute node connections with memoization - function computeNodeConnections(nodeId: string): PhenotypeKsIdMap[] { - if (memo.has(nodeId)) { - return memo.get(nodeId)!; - } - - const node = hierarchicalNodes[nodeId]; - const result: PhenotypeKsIdMap[] = Object.values(endorgans).map(() => ({})); - - if (node.children && node.children.size > 0) { - node.children.forEach(childId => { - const childConnections = computeNodeConnections(childId); - childConnections.forEach((child, index) => { - Object.keys(child).forEach(phenotype => { - if (!result[index][phenotype]) { - result[index][phenotype] = { ksIds: [] }; - } - result[index][phenotype].ksIds = result[index][phenotype].ksIds.concat(child[phenotype].ksIds); - }); - }); - }); - } else if (node.destinationDetails) { - // Add the sub end organs to the connection details - Object.keys(node.destinationDetails).forEach(endOrganIRI => { - const index = organIndexMap[endOrganIRI]; - node.destinationDetails = node.destinationDetails || {}; // Keeps linter happy - if (index !== undefined) { - const knowledgeStatementIds = Array.from(node.destinationDetails[endOrganIRI]) - .filter(ksId => ksId in knowledgeStatements); - - knowledgeStatementIds.forEach(ksId => { - const phenotype = knowledgeStatements[ksId].phenotype ? knowledgeStatements[ksId].phenotype : OTHER_PHENOTYPE_LABEL; - if (!result[index][phenotype]) { - result[index][phenotype] = { ksIds: [] }; - } - result[index][phenotype].ksIds.push(ksId); - }); - } - }); - } - - memo.set(nodeId, result); - return result; - } - computeNodeConnections(hierarchyNode.id) - return memo; + // Apply filters to organs and knowledge statements + const knowledgeStatements = summaryFilterKnowledgeStatements(allKnowledgeStatements, summaryFilters); + + const organIndexMap = Object.values(endorgans).reduce>((map, organ, index) => { + map[organ.id] = index; + return map; + }, {}); + + // Memoization map to store computed results for nodes + const memo = new Map(); + + // Function to compute node connections with memoization + function computeNodeConnections(nodeId: string): PhenotypeKsIdMap[] { + if (memo.has(nodeId)) { + return memo.get(nodeId)!; + } + + const node = hierarchicalNodes[nodeId]; + const result: PhenotypeKsIdMap[] = Object.values(endorgans).map(() => ({})); + + if (node.children && node.children.size > 0) { + node.children.forEach(childId => { + const childConnections = computeNodeConnections(childId); + childConnections.forEach((child, index) => { + Object.keys(child).forEach(phenotype => { + if (!result[index][phenotype]) { + result[index][phenotype] = {ksIds: []}; + } + result[index][phenotype].ksIds = result[index][phenotype].ksIds.concat(child[phenotype].ksIds); + }); + }); + }); + } else if (node.destinationDetails) { + // Add the sub end organs to the connection details + Object.keys(node.destinationDetails).forEach(endOrganIRI => { + const index = organIndexMap[endOrganIRI]; + node.destinationDetails = node.destinationDetails || {}; // Keeps linter happy + if (index !== undefined) { + const knowledgeStatementIds = Array.from(node.destinationDetails[endOrganIRI]) + .filter(ksId => ksId in knowledgeStatements); + + knowledgeStatementIds.forEach(ksId => { + const phenotype = knowledgeStatements[ksId].phenotype ? knowledgeStatements[ksId].phenotype : OTHER_PHENOTYPE_LABEL; + if (!result[index][phenotype]) { + result[index][phenotype] = {ksIds: []}; + } + result[index][phenotype].ksIds.push(ksId); + }); + } + }); + } + + memo.set(nodeId, result); + return result; + } + + computeNodeConnections(hierarchyNode.id) + return memo; } export const getNormalizedValueForMinMax = (value: number, min: number, max: number): number => { - // keep the min 0 always... - // Ex. for situations where min is 4... the value 4 will not be shown... - min = 0; - if (max === 0) return 0; - return max !== min ? (value - min) / (max - min) : 1; + // keep the min 0 always... + // Ex. for situations where min is 4... the value 4 will not be shown... + min = 0; + if (max === 0) return 0; + return max !== min ? (value - min) / (max - min) : 1; } export function getXAxisForHeatmap(endorgan: Organ) { - if (endorgan?.children) { - return Array.from(endorgan.children.values()).map((endOrgan) => endOrgan.name); - } - return [] + if (endorgan?.children) { + return Array.from(endorgan.children.values()).map((endOrgan) => endOrgan.name); + } + return [] } export const getDestinations = (connection: ConnectionSummary): Record => { - return Array.from(connection.endOrgan?.children?.values()).reduce((acc, organ, index) => { - acc[organ.id] = { ...organ, children: new Map(), order: index }; - return acc; - }, {} as Record); + return Array.from(connection.endOrgan?.children?.values()).reduce((acc, organ, index) => { + acc[organ.id] = {...organ, children: new Map(), order: index}; + return acc; + }, {} as Record); }; export const getConnectionDetails = (uniqueKS: KsMapType, connectionPage: number): KnowledgeStatement => { - return uniqueKS !== undefined ? uniqueKS[Object.keys(uniqueKS)[connectionPage - 1]] : {} as KnowledgeStatement; + return uniqueKS !== undefined ? uniqueKS[Object.keys(uniqueKS)[connectionPage - 1]] : {} as KnowledgeStatement; }; diff --git a/yarn.lock b/yarn.lock index bdf027e..83816c2 100644 --- a/yarn.lock +++ b/yarn.lock @@ -4,12 +4,12 @@ "@aashutoshrathi/word-wrap@^1.2.3": version "1.2.6" - resolved "https://registry.yarnpkg.com/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz#bd9154aec9983f77b3a034ecaa015c2e4201f6cf" + resolved "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz" integrity sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA== "@ampproject/remapping@^2.2.0": version "2.2.1" - resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.1.tgz#99e8e11851128b8702cd57c33684f1d0f260b630" + resolved "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz" integrity sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg== dependencies: "@jridgewell/gen-mapping" "^0.3.0" @@ -17,7 +17,7 @@ "@babel/code-frame@^7.0.0", "@babel/code-frame@^7.23.5": version "7.23.5" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.23.5.tgz#9009b69a8c602293476ad598ff53e4562e15c244" + resolved "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz" integrity sha512-CgH3s1a96LipHCmSUmYFPwY7MNx8C3avkq7i4Wl3cfa662ldtUe4VM1TPXX70pfmrlWTb6jLqTYrZyT2ZTJBgA== dependencies: "@babel/highlight" "^7.23.4" @@ -25,12 +25,12 @@ "@babel/compat-data@^7.23.5": version "7.23.5" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.23.5.tgz#ffb878728bb6bdcb6f4510aa51b1be9afb8cfd98" + resolved "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.23.5.tgz" integrity sha512-uU27kfDRlhfKl+w1U6vp16IuvSLtjAxdArVXPa9BvLkrr7CYIsxH5adpHObeAGY/41+syctUWOZ140a2Rvkgjw== "@babel/core@^7.23.5": version "7.23.9" - resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.23.9.tgz#b028820718000f267870822fec434820e9b1e4d1" + resolved "https://registry.npmjs.org/@babel/core/-/core-7.23.9.tgz" integrity sha512-5q0175NOjddqpvvzU+kDiSOAk4PfdO6FvwCWoQ6RO7rTzEe8vlo+4HVfcnAREhD4npMs0e9uZypjTwzZPCf/cw== dependencies: "@ampproject/remapping" "^2.2.0" @@ -51,7 +51,7 @@ "@babel/generator@^7.23.6": version "7.23.6" - resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.23.6.tgz#9e1fca4811c77a10580d17d26b57b036133f3c2e" + resolved "https://registry.npmjs.org/@babel/generator/-/generator-7.23.6.tgz" integrity sha512-qrSfCYxYQB5owCmGLbl8XRpX1ytXlpueOb0N0UmQwA073KZxejgQTzAmJezxvpwQD9uGtK2shHdi55QT+MbjIw== dependencies: "@babel/types" "^7.23.6" @@ -61,7 +61,7 @@ "@babel/helper-compilation-targets@^7.23.6": version "7.23.6" - resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.23.6.tgz#4d79069b16cbcf1461289eccfbbd81501ae39991" + resolved "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.23.6.tgz" integrity sha512-9JB548GZoQVmzrFgp8o7KxdgkTGm6xs9DW0o/Pim72UDjzr5ObUQ6ZzYPqA+g9OTS2bBQoctLJrky0RDCAWRgQ== dependencies: "@babel/compat-data" "^7.23.5" @@ -72,12 +72,12 @@ "@babel/helper-environment-visitor@^7.22.20": version "7.22.20" - resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz#96159db61d34a29dba454c959f5ae4a649ba9167" + resolved "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz" integrity sha512-zfedSIzFhat/gFhWfHtgWvlec0nqB9YEIVrpuwjruLlXfUSnA8cJB0miHKwqDnQ7d32aKo2xt88/xZptwxbfhA== "@babel/helper-function-name@^7.23.0": version "7.23.0" - resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz#1f9a3cdbd5b2698a670c30d2735f9af95ed52759" + resolved "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz" integrity sha512-OErEqsrxjZTJciZ4Oo+eoZqeW9UIiOcuYKRJA4ZAgV9myA+pOXhhmpfNCKjEH/auVfEYVFJ6y1Tc4r0eIApqiw== dependencies: "@babel/template" "^7.22.15" @@ -85,21 +85,21 @@ "@babel/helper-hoist-variables@^7.22.5": version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz#c01a007dac05c085914e8fb652b339db50d823bb" + resolved "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz" integrity sha512-wGjk9QZVzvknA6yKIUURb8zY3grXCcOZt+/7Wcy8O2uctxhplmUPkOdlgoNhmdVee2c92JXbf1xpMtVNbfoxRw== dependencies: "@babel/types" "^7.22.5" "@babel/helper-module-imports@^7.16.7", "@babel/helper-module-imports@^7.22.15": version "7.22.15" - resolved "https://registry.yarnpkg.com/@babel/helper-module-imports/-/helper-module-imports-7.22.15.tgz#16146307acdc40cc00c3b2c647713076464bdbf0" + resolved "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.22.15.tgz" integrity sha512-0pYVBnDKZO2fnSPCrgM/6WMc7eS20Fbok+0r88fp+YtWVLZrp4CkafFGIp+W0VKw4a22sgebPT99y+FDNMdP4w== dependencies: "@babel/types" "^7.22.15" "@babel/helper-module-transforms@^7.23.3": version "7.23.3" - 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resolved "https://registry.yarnpkg.com/@babel/helper-validator-option/-/helper-validator-option-7.23.5.tgz#907a3fbd4523426285365d1206c423c4c5520307" + resolved "https://registry.npmjs.org/@babel/helper-validator-option/-/helper-validator-option-7.23.5.tgz" integrity sha512-85ttAOMLsr53VgXkTbkx8oA6YTfT4q7/HzXSLEYmjcSTJPMPQtvq1BD79Byep5xMUYbGRzEpDsjUf3dyp54IKw== "@babel/helpers@^7.23.9": version "7.23.9" - resolved "https://registry.yarnpkg.com/@babel/helpers/-/helpers-7.23.9.tgz#c3e20bbe7f7a7e10cb9b178384b4affdf5995c7d" + resolved "https://registry.npmjs.org/@babel/helpers/-/helpers-7.23.9.tgz" integrity sha512-87ICKgU5t5SzOT7sBMfCOZQ2rHjRU+Pcb9BoILMYz600W6DkVRLFBPwQ18gwUVvggqXivaUakpnxWQGbpywbBQ== dependencies: "@babel/template" "^7.23.9" @@ -153,7 +153,7 @@ "@babel/highlight@^7.23.4": version "7.23.4" - resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.23.4.tgz#edaadf4d8232e1a961432db785091207ead0621b" + resolved "https://registry.npmjs.org/@babel/highlight/-/highlight-7.23.4.tgz" integrity sha512-acGdbYSfp2WheJoJm/EBBBLh/ID8KDc64ISZ9DYtBmC8/Q204PZJLHyzeB5qMzJ5trcOkybd78M4x2KWsUq++A== dependencies: "@babel/helper-validator-identifier" "^7.22.20" @@ -162,33 +162,33 @@ "@babel/parser@^7.1.0", "@babel/parser@^7.20.7", "@babel/parser@^7.23.9": version "7.23.9" - 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resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" + resolved "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz" integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== yocto-queue@^1.0.0: version "1.0.0" - resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.0.0.tgz#7f816433fb2cbc511ec8bf7d263c3b58a1a3c251" + resolved "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.0.0.tgz" integrity sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g== From 28d12be0dc90d99769dfd612e716c5dd239c7d2f Mon Sep 17 00:00:00 2001 From: afonso Date: Fri, 31 May 2024 16:03:39 +0100 Subject: [PATCH 2/3] ESCKAN-54 feat: Sort phenotype names --- src/services/summaryHeatmapService.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/services/summaryHeatmapService.ts b/src/services/summaryHeatmapService.ts index d88bbda..125f732 100644 --- a/src/services/summaryHeatmapService.ts +++ b/src/services/summaryHeatmapService.ts @@ -63,7 +63,7 @@ export function getAllPhenotypes( }); }); - return Array.from(phenotypeNames); + return Array.from(phenotypeNames).sort(); } export const getNerveFilters = ( From 15812a857c0b409d1d4852f705c0cbfa55a0a4ec Mon Sep 17 00:00:00 2001 From: afonso Date: Fri, 31 May 2024 18:18:32 +0100 Subject: [PATCH 3/3] ESCKAN feat: Natural sort the node children --- src/models/explorer.ts | 6 +++--- src/services/hierarchyService.ts | 23 +++++++++++++++++++++++ 2 files changed, 26 insertions(+), 3 deletions(-) diff --git a/src/models/explorer.ts b/src/models/explorer.ts index 76bbd05..17d2499 100644 --- a/src/models/explorer.ts +++ b/src/models/explorer.ts @@ -280,19 +280,19 @@ export interface HierarchicalNode { uri: string; /** * The children of the node - * @type {Array} + * @type {Set} * @memberof HierarchicalNode */ children: Set; /** * The connection details of the node targetOrgan -> KnowledgeStatementsId - * @type {Record>} + * @type {Record} * @memberof HierarchicalNode */ connectionDetails?: Record; /** * The sub end organs of the node - * @type {Record>} + * @type {Record} * @memberof HierarchicalNode */ destinationDetails?: Record; diff --git a/src/services/hierarchyService.ts b/src/services/hierarchyService.ts index 0cb4af5..bfdcfe7 100644 --- a/src/services/hierarchyService.ts +++ b/src/services/hierarchyService.ts @@ -142,6 +142,25 @@ export const getHierarchicalNodes = (jsonData: JsonData) => { } }); + // Sort the children of each node + Object.values(hierarchicalNodes).forEach((node) => { + if (node.children) { + node.children = new Set( + Array.from(node.children).sort((a, b) => { + const nodeA = hierarchicalNodes[a]; + const nodeB = hierarchicalNodes[b]; + + // First, compare based on whether they have children + if (nodeA.children.size > 0 && nodeB.children.size === 0) return -1; + if (nodeA.children.size === 0 && nodeB.children.size > 0) return 1; + + // If both have children or both don't have children, use natural sort + return naturalSort(nodeA.name, nodeB.name); + }), + ); + } + }); + return hierarchicalNodes; }; @@ -198,3 +217,7 @@ export const getOrgans = (jsonData: JsonData): Record => { return organsRecord; }; + +const naturalSort = (a: string, b: string) => { + return a.localeCompare(b, undefined, { numeric: true, sensitivity: 'base' }); +};