From 2ea0be00f04f73e72f0008f3ecd5f2d281731180 Mon Sep 17 00:00:00 2001
From: "Hartung, Michael" <michael.hartung@uni-hamburg.de>
Date: Fri, 5 May 2023 16:00:52 +0200
Subject: [PATCH] hide connector nodes in legend if none in network
---
.../analysis-panel.component.ts | 682 +++++++++++-------
.../network-legend.component.ts | 65 +-
.../legend-service/legend-service.service.ts | 7 +
src/index.html | 2 +-
4 files changed, 481 insertions(+), 275 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 26c8b639..a616c00f 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -9,9 +9,12 @@ import {
Output,
SimpleChanges,
ViewChild,
-} from '@angular/core';
-import {HttpClient} from '@angular/common/http';
-import {algorithmNames, AnalysisService} from '../../services/analysis/analysis.service';
+} from "@angular/core";
+import { HttpClient } from "@angular/common/http";
+import {
+ algorithmNames,
+ AnalysisService,
+} from "../../services/analysis/analysis.service";
import {
Drug,
NodeAttributeMap,
@@ -23,22 +26,26 @@ import {
Tissue,
Wrapper,
NodeInteraction,
-} from '../../interfaces';
-import {NetworkSettings} from '../../network-settings';
-import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
-import {mapCustomEdge, mapNetexEdge, ProteinNetwork} from 'src/app/main-network';
-import {DrugstoneConfigService} from 'src/app/services/drugstone-config/drugstone-config.service';
-import {NetworkHandlerService} from 'src/app/services/network-handler/network-handler.service';
-import {LegendService} from 'src/app/services/legend-service/legend-service.service';
-import {LoadingScreenService} from 'src/app/services/loading-screen/loading-screen.service';
-import {version} from '../../../version';
-import {downloadCSV} from 'src/app/utils';
+} from "../../interfaces";
+import { NetworkSettings } from "../../network-settings";
+import { NetexControllerService } from "src/app/services/netex-controller/netex-controller.service";
+import {
+ mapCustomEdge,
+ mapNetexEdge,
+ ProteinNetwork,
+} from "src/app/main-network";
+import { DrugstoneConfigService } from "src/app/services/drugstone-config/drugstone-config.service";
+import { NetworkHandlerService } from "src/app/services/network-handler/network-handler.service";
+import { LegendService } from "src/app/services/legend-service/legend-service.service";
+import { LoadingScreenService } from "src/app/services/loading-screen/loading-screen.service";
+import { version } from "../../../version";
+import { downloadCSV } from "src/app/utils";
declare var vis: any;
interface Scored {
- score: number; // Normalized or unnormalized (whichever user selects, will be displayed in the table)
- rawScore: number; // Unnormalized (kept to restore unnormalized value)
+ score: number; // Normalized or unnormalized (whichever user selects, will be displayed in the table)
+ rawScore: number; // Unnormalized (kept to restore unnormalized value)
rank: number;
}
@@ -46,23 +53,25 @@ interface Seeded {
isSeed: boolean;
}
-
@Component({
- selector: 'app-analysis-panel',
- templateUrl: './analysis-panel.component.html',
- styleUrls: ['./analysis-panel.component.scss'],
+ selector: "app-analysis-panel",
+ templateUrl: "./analysis-panel.component.html",
+ styleUrls: ["./analysis-panel.component.scss"],
})
-export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit {
-
- @ViewChild('networkWithLegend', {static: false}) networkWithLegendEl: ElementRef;
+export class AnalysisPanelComponent
+ implements OnInit, OnChanges, AfterViewInit
+{
+ @ViewChild("networkWithLegend", { static: false })
+ networkWithLegendEl: ElementRef;
@Input() token: string | null = null;
@Input() tokenType: string | null = null;
-
@Output() tokenChange = new EventEmitter<string | null>();
@Output() showDetailsChange = new EventEmitter<Wrapper>();
@Output() setInputNetwork = new EventEmitter<any>();
- @Output() visibleItems = new EventEmitter<[any[], [Node[], Tissue], NodeInteraction[]]>();
+ @Output() visibleItems = new EventEmitter<
+ [any[], [Node[], Tissue], NodeInteraction[]]
+ >();
public task: Task | null = null;
public result: any = null;
@@ -71,10 +80,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public algorithmDefault = undefined;
public network: any;
- public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
+ public nodeData: { nodes: any; edges: any } = { nodes: null, edges: null };
// private drugNodes: any[] = [];
// private drugEdges: any[] = [];
- public tab: 'meta' | 'network' | 'table' = 'network';
+ public tab: "meta" | "network" | "table" = "network";
private proteins: any;
public effects: any;
@@ -85,15 +94,15 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public tableNormalize = false;
public tableHasScores = false;
- public LegendContext: LegendContext = 'drugTarget';
+ public LegendContext: LegendContext = "drugTarget";
public expressionExpanded = false;
public selectedTissue: Tissue | null = null;
public algorithmNames = algorithmNames;
- public tableDrugScoreTooltip = '';
- public tableProteinScoreTooltip = '';
+ public tableDrugScoreTooltip = "";
+ public tableProteinScoreTooltip = "";
public versionString = undefined;
@@ -101,18 +110,24 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public loading = false;
- constructor(public legendService: LegendService, public networkHandler: NetworkHandlerService, public drugstoneConfig: DrugstoneConfigService, private http: HttpClient, public analysis: AnalysisService, public netex: NetexControllerService, public loadingScreen: LoadingScreenService) {
+ constructor(
+ public legendService: LegendService,
+ public networkHandler: NetworkHandlerService,
+ public drugstoneConfig: DrugstoneConfigService,
+ private http: HttpClient,
+ public analysis: AnalysisService,
+ public netex: NetexControllerService,
+ public loadingScreen: LoadingScreenService
+ ) {
try {
this.versionString = version;
- } catch (e) {
- }
+ } catch (e) {}
}
- async ngOnInit() {
- }
+ async ngOnInit() {}
ngAfterViewInit() {
- this.networkHandler.setActiveNetwork('analysis');
+ this.networkHandler.setActiveNetwork("analysis");
}
async ngOnChanges(changes: SimpleChanges) {
@@ -127,53 +142,70 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.resetEmitter.emit(true);
}
- private setNetworkListeners(){
- this.networkHandler.activeNetwork.networkInternal.on('dragEnd', (properties) => {
- const node_ids = this.networkHandler.activeNetwork.networkInternal.getSelectedNodes();
- if (node_ids.length === 0 || !this.networkHandler.shiftDown) {
- return;
- }
- this.analysis.addNodesByIdsToSelection(node_ids);
- this.networkHandler.activeNetwork.networkInternal.unselectAll();
- });
- this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
- this.showDetailsChange.emit(null);
- });
- this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
- const nodeIds: Array<string> = properties.nodes;
- if (nodeIds.length > 0) {
- const nodeId = nodeIds[0];
- const node = this.nodeData.nodes.get(nodeId);
- if (node.drugstoneId === undefined || node.nodeType === 'drug' || node.drugstoneType !== 'protein') {
- this.analysis.unmappedNodeToast();
+ private setNetworkListeners() {
+ this.networkHandler.activeNetwork.networkInternal.on(
+ "dragEnd",
+ (properties) => {
+ const node_ids =
+ this.networkHandler.activeNetwork.networkInternal.getSelectedNodes();
+ if (node_ids.length === 0 || !this.networkHandler.shiftDown) {
return;
}
- const wrapper = getWrapperFromNode(node);
- if (this.analysis.inSelection(wrapper)) {
- this.analysis.removeItems([wrapper]);
- this.analysis.getCount();
- } else {
- this.analysis.addItems([wrapper]);
- this.analysis.getCount();
+ this.analysis.addNodesByIdsToSelection(node_ids);
+ this.networkHandler.activeNetwork.networkInternal.unselectAll();
+ }
+ );
+ this.networkHandler.activeNetwork.networkInternal.on(
+ "deselectNode",
+ (properties) => {
+ this.showDetailsChange.emit(null);
+ }
+ );
+ this.networkHandler.activeNetwork.networkInternal.on(
+ "doubleClick",
+ (properties) => {
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ if (
+ node.drugstoneId === undefined ||
+ node.nodeType === "drug" ||
+ node.drugstoneType !== "protein"
+ ) {
+ this.analysis.unmappedNodeToast();
+ return;
+ }
+ const wrapper = getWrapperFromNode(node);
+ if (this.analysis.inSelection(wrapper)) {
+ this.analysis.removeItems([wrapper]);
+ this.analysis.getCount();
+ } else {
+ this.analysis.addItems([wrapper]);
+ this.analysis.getCount();
+ }
}
}
- });
-
- this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
- if (properties.nodes.length === 0 && properties.edges.length === 1) {
- // clicked on one edge
- const edgeId = properties.edges[0];
- this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
- } else {
- this.networkHandler.activeNetwork.activeEdge = null;
- const selectedNodes = this.nodeData.nodes.get(properties.nodes);
- if (selectedNodes.length > 0) {
- this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
+ );
+
+ this.networkHandler.activeNetwork.networkInternal.on(
+ "click",
+ (properties) => {
+ if (properties.nodes.length === 0 && properties.edges.length === 1) {
+ // clicked on one edge
+ const edgeId = properties.edges[0];
+ this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
} else {
- this.showDetailsChange.emit(null);
+ this.networkHandler.activeNetwork.activeEdge = null;
+ const selectedNodes = this.nodeData.nodes.get(properties.nodes);
+ if (selectedNodes.length > 0) {
+ this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
+ } else {
+ this.showDetailsChange.emit(null);
+ }
}
}
- });
+ );
this.analysis.subscribeList((items, selected) => {
// return if analysis panel is closed or no nodes are loaded
if (!this.token) {
@@ -187,10 +219,15 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (!node) {
continue;
}
- const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
+ const pos =
+ this.networkHandler.activeNetwork.networkInternal.getPositions([
+ item.id,
+ ]);
node.x = pos[item.id].x;
node.y = pos[item.id].y;
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds
+ ? this.networkHandler.activeNetwork.seedMap[node.id]
+ : false;
const nodeStyled = NetworkSettings.getNodeStyle(
node,
this.drugstoneConfig.currentConfig(),
@@ -206,8 +243,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
const proteinSelection = this.tableSelectedProteins;
for (const item of items) {
// TODO: Refactor!
- const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.id);
- const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ const found = proteinSelection.findIndex(
+ (i) => getProteinNodeId(i) === item.id
+ );
+ const tableItem = this.tableProteins.find(
+ (i) => getProteinNodeId(i) === item.id
+ );
if (selected && found === -1 && tableItem) {
proteinSelection.push(tableItem);
}
@@ -220,7 +261,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// else: selected is null
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds
+ ? this.networkHandler.activeNetwork.seedMap[node.id]
+ : false;
if (!isSeed) {
return;
}
@@ -238,7 +281,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
const proteinSelection = [];
for (const item of items) {
- const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ const tableItem = this.tableProteins.find(
+ (i) => getProteinNodeId(i) === item.id
+ );
if (tableItem) {
proteinSelection.push(tableItem);
}
@@ -248,7 +293,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
});
}
- private rankTable(table: Array<Drug & Scored> | Array<Node & Scored & Seeded>) {
+ private rankTable(
+ table: Array<Drug & Scored> | Array<Node & Scored & Seeded>
+ ) {
let lastRank = 1;
for (let idx = 0; idx < table.length; idx++) {
if (idx === 0) {
@@ -265,16 +312,15 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
private async refreshView() {
this.loading = true;
this.loadingScreen.stateUpdate(true);
- this.getView(this.token).then(async view => {
+ this.getView(this.token).then(async (view) => {
this.task = view;
this.result = view;
this.drugstoneConfig.set_analysisConfig(view.config);
this.analysis.switchSelection(this.token);
this.loadingScreen.stateUpdate(false);
-
// Reset
- this.nodeData = {nodes: null, edges: null};
+ this.nodeData = { nodes: null, edges: null };
// this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
// this.networkHandler.activeNetwork.networkInternal = null;
// Create+
@@ -284,34 +330,56 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (this.drugstoneConfig.config.autofillEdges && nodes.length) {
const node_map = {};
- nodes.filter(n => n.drugstoneType === 'protein').forEach(node => {
- if (typeof node.drugstoneId === 'string') {
- if (node_map[node.drugstoneId]) {
- node_map[node.drugstoneId].push(node.id);
- } else {
- node_map[node.drugstoneId] = [node.id];
- }
- } else {
- node.drugstoneId.forEach(n => {
- if (node_map[n]) {
- node_map[n].push(node.id);
+ nodes
+ .filter((n) => n.drugstoneType === "protein")
+ .forEach((node) => {
+ if (typeof node.drugstoneId === "string") {
+ if (node_map[node.drugstoneId]) {
+ node_map[node.drugstoneId].push(node.id);
} else {
- node_map[n] = [node.id];
+ node_map[node.drugstoneId] = [node.id];
}
- });
- }
- });
- const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein, this.drugstoneConfig.config.licensedDatasets);
- edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.currentConfig(), node_map)).flatMap(e => e));
+ } else {
+ node.drugstoneId.forEach((n) => {
+ if (node_map[n]) {
+ node_map[n].push(node.id);
+ } else {
+ node_map[n] = [node.id];
+ }
+ });
+ }
+ });
+ const netexEdges = await this.netex.fetchEdges(
+ nodes,
+ this.drugstoneConfig.config.interactionProteinProtein,
+ this.drugstoneConfig.config.licensedDatasets
+ );
+ edges.push(
+ ...netexEdges
+ .map((netexEdge) =>
+ mapNetexEdge(
+ netexEdge,
+ this.drugstoneConfig.currentConfig(),
+ node_map
+ )
+ )
+ .flatMap((e) => e)
+ );
}
const edge_map = {};
- edges = edges.filter(edge => {
- if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1) {
+ edges = edges.filter((edge) => {
+ if (
+ edge_map[edge.to] &&
+ edge_map[edge.to].indexOf(edge.from) !== -1
+ ) {
return false;
}
- if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !== -1) {
+ if (
+ edge_map[edge.from] &&
+ edge_map[edge.from].indexOf(edge.to) !== -1
+ ) {
return false;
}
if (!edge_map[edge.from]) {
@@ -324,15 +392,22 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// @ts-ignore
if (!this.drugstoneConfig.selfReferences) {
- edges = edges.filter(el => el.from !== el.to);
+ edges = edges.filter((el) => el.from !== el.to);
}
- this.networkHandler.activeNetwork.inputNetwork = {nodes: nodes, edges: edges};
+ this.networkHandler.activeNetwork.inputNetwork = {
+ nodes: nodes,
+ edges: edges,
+ };
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
- const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
+ const container =
+ this.networkHandler.activeNetwork.networkEl.nativeElement;
const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
+ const options = NetworkSettings.getOptions(
+ isBig ? "analysis-big" : "analysis",
+ this.drugstoneConfig.currentConfig()
+ );
// @ts-ignore
options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
// @ts-ignore
@@ -343,19 +418,31 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (this.drugstoneConfig.config.physicsOn) {
this.drugstoneConfig.config.physicsOn = !isBig;
}
- this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
+ this.networkHandler.activeNetwork.networkInternal = new vis.Network(
+ container,
+ this.nodeData,
+ options
+ );
if (isBig) {
resolve(nodes);
}
- this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
- if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
- this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
+ this.networkHandler.activeNetwork.networkInternal.once(
+ "stabilizationIterationsDone",
+ async () => {
+ if (
+ !this.drugstoneConfig.config.physicsOn ||
+ this.networkHandler.activeNetwork.isBig()
+ ) {
+ this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
+ }
+ this.networkHandler
+ .updateAdjacentNodes(this.networkHandler.activeNetwork.isBig())
+ .then(() => {
+ resolve(nodes);
+ });
}
- this.networkHandler.updateAdjacentNodes(this.networkHandler.activeNetwork.isBig()).then(() => {
- resolve(nodes);
- });
- });
+ );
}).then(() => {
this.setNetworkListeners();
this.emitVisibleItems(true);
@@ -363,79 +450,84 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
});
}
-
private async refreshTask() {
this.loadingScreen.stateUpdate(true);
this.task = await this.getTask(this.token);
this.analysis.switchSelection(this.token);
- if (this.task.info.algorithm === 'degree') {
+ if (this.task.info.algorithm === "degree") {
this.tableDrugScoreTooltip =
- 'Normalized number of direct interactions of the drug with the seeds. ' +
- 'The higher the score, the more relevant the drug.';
+ "Normalized number of direct interactions of the drug with the seeds. " +
+ "The higher the score, the more relevant the drug.";
this.tableProteinScoreTooltip =
- 'Normalized number of direct interactions of the protein with the seeds. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'closeness' || this.task.info.algorithm === 'quick' || this.task.info.algorithm === 'super') {
+ "Normalized number of direct interactions of the protein with the seeds. " +
+ "The higher the score, the more relevant the protein.";
+ } else if (
+ this.task.info.algorithm === "closeness" ||
+ this.task.info.algorithm === "quick" ||
+ this.task.info.algorithm === "super"
+ ) {
this.tableDrugScoreTooltip =
- 'Normalized inverse mean distance of the drug to the seeds. ' +
- 'The higher the score, the more relevant the drug.';
+ "Normalized inverse mean distance of the drug to the seeds. " +
+ "The higher the score, the more relevant the drug.";
this.tableProteinScoreTooltip =
- 'Normalized inverse mean distance of the protein to the seeds. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'trustrank') {
+ "Normalized inverse mean distance of the protein to the seeds. " +
+ "The higher the score, the more relevant the protein.";
+ } else if (this.task.info.algorithm === "trustrank") {
this.tableDrugScoreTooltip =
- 'Amount of ‘trust’ on the drug at termination of the algorithm. ' +
- 'The higher the score, the more relevant the drug.';
+ "Amount of ‘trust’ on the drug at termination of the algorithm. " +
+ "The higher the score, the more relevant the drug.";
this.tableProteinScoreTooltip =
- 'Amount of ‘trust’ on the protein at termination of the algorithm. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'proximity') {
+ "Amount of ‘trust’ on the protein at termination of the algorithm. " +
+ "The higher the score, the more relevant the protein.";
+ } else if (this.task.info.algorithm === "proximity") {
this.tableDrugScoreTooltip =
- 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
- 'The lower the score, the more relevant the drug.';
+ "Empirical z-score of mean minimum distance between the drug’s targets and the seeds. " +
+ "The lower the score, the more relevant the drug.";
this.tableProteinScoreTooltip =
- 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
- 'The lower the score, the more relevant the drug.';
+ "Empirical z-score of mean minimum distance between the drug’s targets and the seeds. " +
+ "The lower the score, the more relevant the drug.";
}
if (this.task && this.task.info && this.task.info.done) {
-
this.loading = true;
- this.netex.getTaskResult(this.token).then(async result => {
- if (this.networkHandler.activeNetwork.networkType !== 'analysis') {
+ this.netex.getTaskResult(this.token).then(async (result) => {
+ if (this.networkHandler.activeNetwork.networkType !== "analysis") {
return;
}
this.drugstoneConfig.set_analysisConfig(result.parameters.config);
this.analysis.switchSelection(this.token);
this.result = result;
- if (this.result.parameters.target === 'drug') {
- this.legendService.add_to_context('drug');
+ if (this.result.parameters.target === "drug") {
+ this.legendService.add_to_context("drug");
} else {
- this.legendService.add_to_context('drugTarget');
+ this.legendService.add_to_context("drugTarget");
}
const nodeAttributes = this.result.nodeAttributes || {};
- const analysisNetwork = this.networkHandler.networks['analysis'];
+ const analysisNetwork = this.networkHandler.networks["analysis"];
analysisNetwork.seedMap = nodeAttributes.isSeed || {};
// Reset
- this.nodeData = {nodes: null, edges: null};
- analysisNetwork.networkEl.nativeElement.innerHTML = '';
+ this.nodeData = { nodes: null, edges: null };
+ analysisNetwork.networkEl.nativeElement.innerHTML = "";
analysisNetwork.networkInternal = null;
// Create
- await this.createNetwork(this.result).then(nw => {
+ await this.createNetwork(this.result).then((nw) => {
return new Promise<any>((resolve, reject) => {
- if (this.networkHandler.activeNetwork.networkType !== 'analysis') {
+ if (this.networkHandler.activeNetwork.networkType !== "analysis") {
return;
}
const nodes = nw.nodes;
const edges = nw.edges;
- analysisNetwork.inputNetwork = {nodes: nodes, edges: edges};
+ analysisNetwork.inputNetwork = { nodes: nodes, edges: edges };
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
const container = analysisNetwork.networkEl.nativeElement;
const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
+ const options = NetworkSettings.getOptions(
+ isBig ? "analysis-big" : "analysis",
+ this.drugstoneConfig.currentConfig()
+ );
// @ts-ignore
options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
// @ts-ignore
@@ -446,60 +538,94 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (this.drugstoneConfig.config.physicsOn) {
this.drugstoneConfig.config.physicsOn = !isBig;
}
- analysisNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
+ analysisNetwork.networkInternal = new vis.Network(
+ container,
+ this.nodeData,
+ options
+ );
if (isBig) {
resolve(nodes);
}
- analysisNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
- if (!this.drugstoneConfig.config.physicsOn || analysisNetwork.isBig()) {
- analysisNetwork.updatePhysicsEnabled(false);
+ analysisNetwork.networkInternal.once(
+ "stabilizationIterationsDone",
+ async () => {
+ if (
+ !this.drugstoneConfig.config.physicsOn ||
+ analysisNetwork.isBig()
+ ) {
+ analysisNetwork.updatePhysicsEnabled(false);
+ }
+ this.networkHandler
+ .updateAdjacentNodes(analysisNetwork.isBig())
+ .then(() => {
+ resolve(nodes);
+ });
}
- this.networkHandler.updateAdjacentNodes(analysisNetwork.isBig()).then(() => {
- resolve(nodes);
+ );
+ })
+ .then((nodes) => {
+ this.tableDrugs = nodes.filter(
+ (e) => e.drugstoneId && e.drugstoneType === "drug"
+ );
+ this.tableDrugs.forEach((r) => {
+ r.rawScore = r.score;
});
- });
- }).then(nodes => {
-
- this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
- this.tableDrugs.forEach((r) => {
- r.rawScore = r.score;
- });
- // @ts-ignore
- this.tableDrugs.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableDrugs);
- this.tableProteins = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'protein');
- this.tableSelectedProteins = [];
- this.tableProteins.forEach((r) => {
- r.rawScore = r.score;
- r.isSeed = analysisNetwork.seedMap[r.id];
- const wrapper = getWrapperFromNode(r);
- if (this.analysis.inSelection(wrapper)) {
- this.tableSelectedProteins.push(r);
+ // @ts-ignore
+ this.tableDrugs.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableDrugs);
+ this.tableProteins = nodes.filter(
+ (e) => e.drugstoneId && e.drugstoneType === "protein"
+ );
+ this.tableSelectedProteins = [];
+ this.tableProteins.forEach((r) => {
+ r.rawScore = r.score;
+ r.isSeed = analysisNetwork.seedMap[r.id];
+ const wrapper = getWrapperFromNode(r);
+ if (this.analysis.inSelection(wrapper)) {
+ this.tableSelectedProteins.push(r);
+ }
+ });
+ this.tableProteins.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableProteins);
+
+ this.tableHasScores =
+ [
+ "trustrank",
+ "closeness",
+ "degree",
+ "betweenness",
+ "quick",
+ "super",
+ ].indexOf(this.task.info.algorithm) !== -1;
+ if (this.tableHasScores) {
+ this.toggleNormalization(true);
}
- });
- this.tableProteins.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableProteins);
-
- this.tableHasScores = ['trustrank', 'closeness', 'degree', 'betweenness', 'quick', 'super']
- .indexOf(this.task.info.algorithm) !== -1;
- if (this.tableHasScores) {
- this.toggleNormalization(true);
- }
- analysisNetwork.networkInternal.setData({nodes: undefined, edge: undefined});
- setTimeout(() => {
- analysisNetwork.networkInternal.setData(this.nodeData);
- }, 1000);
- this.setNetworkListeners();
- this.emitVisibleItems(true);
- }).then(() => {
- if (!['quick', 'super', 'connect', 'connectSelected'].includes(this.task.info.algorithm)) {
- return;
- }
- this.netex.getAlgorithmDefaults(this.task.info.algorithm).then(response => {
- this.algorithmDefault = response;
- });
- }).catch(console.error);
+ analysisNetwork.networkInternal.setData({
+ nodes: undefined,
+ edge: undefined,
+ });
+ setTimeout(() => {
+ analysisNetwork.networkInternal.setData(this.nodeData);
+ }, 1000);
+ this.setNetworkListeners();
+ this.emitVisibleItems(true);
+ })
+ .then(() => {
+ if (
+ !["quick", "super", "connect", "connectSelected"].includes(
+ this.task.info.algorithm
+ )
+ ) {
+ return;
+ }
+ this.netex
+ .getAlgorithmDefaults(this.task.info.algorithm)
+ .then((response) => {
+ this.algorithmDefault = response;
+ });
+ })
+ .catch(console.error);
});
this.loadingScreen.stateUpdate(false);
});
@@ -508,7 +634,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
private async refresh() {
if (this.token) {
- if (this.tokenType === 'view') {
+ if (this.tokenType === "view") {
this.networkHandler.showSeedsButton = false;
await this.refreshView();
} else {
@@ -516,39 +642,47 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
await this.refreshTask();
}
}
-
}
public emitVisibleItems(on: boolean) {
if (on) {
- this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.selectedTissue], this.nodeData.edges]);
+ this.visibleItems.emit([
+ this.nodeData.nodes,
+ [this.proteins, this.selectedTissue],
+ this.nodeData.edges,
+ ]);
} else {
this.visibleItems.emit(null);
}
}
private async getView(token: string): Promise<any> {
- return await this.http.get(`${this.netex.getBackend()}view/?token=${token}`).toPromise();
+ return await this.http
+ .get(`${this.netex.getBackend()}view/?token=${token}`)
+ .toPromise();
}
private async getTask(token: string): Promise<any> {
- return await this.http.get(`${this.netex.getBackend()}task/?token=${token}`).toPromise();
+ return await this.http
+ .get(`${this.netex.getBackend()}task/?token=${token}`)
+ .toPromise();
}
close() {
- const analysisNetwork = this.networkHandler.networks['analysis'];
+ const analysisNetwork = this.networkHandler.networks["analysis"];
analysisNetwork.gradientMap = {};
this.drugstoneConfig.remove_analysisConfig();
this.expressionExpanded = false;
this.expressionMap = undefined;
analysisNetwork.seedMap = {};
analysisNetwork.highlightSeeds = false;
- this.analysis.switchSelection('main');
+ this.legendService.networkHasConnector = false;
+ this.analysis.switchSelection("main");
// this.analysis.resetSelection();
this.token = null;
this.tokenChange.emit(this.token);
- this.legendService.remove_from_context('drug');
- this.legendService.remove_from_context('drugTarget');
+ this.legendService.remove_from_context("drug");
+ this.legendService.remove_from_context("drugTarget");
this.emitVisibleItems(false);
}
@@ -557,30 +691,30 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
const normalizeFn = (table) => {
let max = 0;
- table.forEach(i => {
+ table.forEach((i) => {
if (i.rawScore > max) {
max = i.rawScore;
}
});
- table.forEach(i => {
+ table.forEach((i) => {
i.score = i.rawScore / max;
});
};
const unnormalizeFn = (table) => {
- table.forEach(i => {
+ table.forEach((i) => {
i.score = i.rawScore;
});
};
if (normalize) {
normalizeFn(this.tableProteins);
- if (this.task.info.target === 'drug') {
+ if (this.task.info.target === "drug") {
normalizeFn(this.tableDrugs);
}
} else {
unnormalizeFn(this.tableProteins);
- if (this.task.info.target === 'drug') {
+ if (this.task.info.target === "drug") {
unnormalizeFn(this.tableDrugs);
}
}
@@ -595,11 +729,22 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
});
- if ('score' in data[0]) {
- data = data.sort((a, b) => b['score'] - a['score']);
+ if ("score" in data[0]) {
+ data = data.sort((a, b) => b["score"] - a["score"]);
}
- const columns = ['label', 'symbol', 'uniprot', 'ensg', 'entrez', 'proteinName', 'isSeed', 'score', 'rank', 'status'];
+ const columns = [
+ "label",
+ "symbol",
+ "uniprot",
+ "ensg",
+ "entrez",
+ "proteinName",
+ "isSeed",
+ "score",
+ "rank",
+ "status",
+ ];
downloadCSV(data, columns, `drugstone_${view}`);
}
@@ -609,7 +754,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
* @param result
* @returns
*/
- public async createNetwork(result: any): Promise<{ edges: any[]; nodes: any[]; }> {
+ public async createNetwork(
+ result: any
+ ): Promise<{ edges: any[]; nodes: any[] }> {
const identifier = this.drugstoneConfig.currentConfig().identifier;
// add drugGroup and foundNodesGroup for added nodes
@@ -625,47 +772,84 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
network.nodes = [...new Set<string>(network.nodes)];
const details = attributes.details || {};
const nodeIdMap = {};
+ Object.entries(details)
// @ts-ignore
- Object.entries(details).filter(e => e[1].drugstoneType === 'protein').forEach(e => {
- // @ts-ignore
- e[1].drugstoneId.forEach(id => {
- nodeIdMap[id] = e[1][identifier][0];
+ .filter((e) => e[1].drugstoneType === "protein")
+ .forEach((e) => {
+ // @ts-ignore
+ e[1].drugstoneId.forEach((id) => {
+ nodeIdMap[id] = e[1][identifier][0];
+ });
});
- });
for (const nodeId of network.nodes) {
if (details[nodeId]) {
const nodeDetails = details[nodeId];
- nodeDetails.id = nodeDetails.id ? nodeDetails.id : (typeof nodeDetails.drugstoneId === 'string' ? nodeDetails.drugstoneId : nodeDetails.drugstoneId[0]);
- if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'protein') {
+ nodeDetails.id = nodeDetails.id
+ ? nodeDetails.id
+ : typeof nodeDetails.drugstoneId === "string"
+ ? nodeDetails.drugstoneId
+ : nodeDetails.drugstoneId[0];
+ if (
+ nodeDetails.drugstoneId &&
+ nodeDetails.drugstoneType === "protein"
+ ) {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
// FIXME connectorNodes are not visualized correctly
- nodeDetails.group = result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1 ? 'foundNode' : (nodeDetails.group ? nodeDetails.group : 'connectorNode');
- nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
- nodeDetails.id = nodeDetails[identifier][0] ? nodeDetails[identifier][0] : nodeDetails.id;
+ nodeDetails.group =
+ result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1
+ ? "foundNode"
+ : nodeDetails.group
+ ? nodeDetails.group
+ : "connectorNode";
+ nodeDetails.label = nodeDetails.label
+ ? nodeDetails.label
+ : nodeDetails[identifier];
+ nodeDetails.id = nodeDetails[identifier][0]
+ ? nodeDetails[identifier][0]
+ : nodeDetails.id;
this.proteins.push(nodeDetails);
- } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'drug') {
+ } else if (
+ nodeDetails.drugstoneId &&
+ nodeDetails.drugstoneType === "drug"
+ ) {
// node is drug, was found during analysis
- nodeDetails.type = 'Drug';
- nodeDetails.group = 'foundDrug';
+ nodeDetails.type = "Drug";
+ nodeDetails.group = "foundDrug";
} else {
// node is custom input from user, could not be mapped to backend protein
- nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'default';
- nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
+ nodeDetails.group = nodeDetails.group ? nodeDetails.group : "default";
+ nodeDetails.label = nodeDetails.label
+ ? nodeDetails.label
+ : nodeDetails[identifier];
}
// further analysis and the button function can be used to highlight seeds
// option to use scores[node] as gradient, but sccores are very small
- nodes.push(NetworkSettings.getNodeStyle(nodeDetails as Node, this.drugstoneConfig.currentConfig(), false, false, 1, this.networkHandler.activeNetwork.nodeRenderer));
+ nodes.push(
+ NetworkSettings.getNodeStyle(
+ nodeDetails as Node,
+ this.drugstoneConfig.currentConfig(),
+ false,
+ false,
+ 1,
+ this.networkHandler.activeNetwork.nodeRenderer
+ )
+ );
} else {
- console.log('Missing details for ' + nodeId);
+ console.log("Missing details for " + nodeId);
}
}
const uniqEdges = [];
for (const edge of network.edges) {
- const e = mapCustomEdge(edge, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
- e.from = e.from[0] === 'p' && nodeIdMap[e.from] ? nodeIdMap[e.from] : e.from;
- e.to = e.to[0] === 'p' && nodeIdMap[e.to] ? nodeIdMap[e.to] : e.to;
- const hash = e.from + '_' + e.to;
+ const e = mapCustomEdge(
+ edge,
+ this.drugstoneConfig.currentConfig(),
+ this.drugstoneConfig
+ );
+ e.from =
+ e.from[0] === "p" && nodeIdMap[e.from] ? nodeIdMap[e.from] : e.from;
+ e.to = e.to[0] === "p" && nodeIdMap[e.to] ? nodeIdMap[e.to] : e.to;
+ const hash = e.from + "_" + e.to;
if (uniqEdges.indexOf(hash) === -1) {
uniqEdges.push(hash);
edges.push(e);
@@ -673,24 +857,35 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
// remove self-edges/loops
if (!this.drugstoneConfig.currentConfig().selfReferences) {
- edges = edges.filter(el => el.from !== el.to);
+ edges = edges.filter((el) => el.from !== el.to);
}
- return {
+
+ this.legendService.networkHasConnector =
+ nodes.filter((node) => node.group === "connectorNode").length > 0;
+
+ return {
nodes,
edges,
};
}
getResultNodes() {
- if (this.nodeData && this.nodeData['nodes']) {
- return this.nodeData['nodes'].get();
+ if (this.nodeData && this.nodeData["nodes"]) {
+ return this.nodeData["nodes"].get();
}
return [];
}
getResultEdges() {
- if (this.nodeData && this.nodeData['edges']) {
- return this.nodeData['edges'].get().filter(e => !e.id || !e.groupName || (typeof e.from === 'string' && typeof e.to === 'string'));
+ if (this.nodeData && this.nodeData["edges"]) {
+ return this.nodeData["edges"]
+ .get()
+ .filter(
+ (e) =>
+ !e.id ||
+ !e.groupName ||
+ (typeof e.from === "string" && typeof e.to === "string")
+ );
}
return [];
}
@@ -728,5 +923,4 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public openBugreport() {
this.drugstoneConfig.showBugreport = true;
}
-
}
diff --git a/src/app/components/network/network-legend/network-legend.component.ts b/src/app/components/network/network-legend/network-legend.component.ts
index 7db97954..8dbafa89 100644
--- a/src/app/components/network/network-legend/network-legend.component.ts
+++ b/src/app/components/network/network-legend/network-legend.component.ts
@@ -1,38 +1,37 @@
-import {Component, Input, OnInit} from '@angular/core';
-import { LegendContext } from 'src/app/interfaces';
-import { DrugstoneConfigService } from 'src/app/services/drugstone-config/drugstone-config.service';
-import {IConfig} from '../../../config';
-import {LegendService} from "src/app/services/legend-service/legend-service.service";
-import { NetworkHandlerService } from 'src/app/services/network-handler/network-handler.service';
+import { Component, Input, OnInit } from "@angular/core";
+import { LegendContext } from "src/app/interfaces";
+import { DrugstoneConfigService } from "src/app/services/drugstone-config/drugstone-config.service";
+import { IConfig } from "../../../config";
+import { LegendService } from "src/app/services/legend-service/legend-service.service";
+import { NetworkHandlerService } from "src/app/services/network-handler/network-handler.service";
@Component({
- selector: 'app-network-legend',
- templateUrl: './network-legend.component.html',
- styleUrls: ['./network-legend.component.scss']
+ selector: "app-network-legend",
+ templateUrl: "./network-legend.component.html",
+ styleUrls: ["./network-legend.component.scss"],
})
export class NetworkLegendComponent implements OnInit {
-
- _context = 'explorer';
+ _context = "explorer";
_emptyEdgeConfig = false;
- @Input() set context (value: LegendContext) {
- this._context = value
+ @Input() set context(value: LegendContext) {
+ this._context = value;
this._emptyEdgeConfig = this.checkIfEdgeConfigEmpty();
- };
+ }
@Input() config: IConfig;
private contextEdgeGroupsToDelete = {
- 'explorer': ['default'],
- 'adjacentDrugs': ['default'],
- 'adjacentDisorders': ['default'],
- 'adjacentDrugsAndDisorders' :['default'],
- 'drugTarget': ['default'],
- 'drug': ['default'],
- 'drugTargetAndSeeds': ['default'],
- 'drugAndSeeds': ['default']
- }
+ explorer: ["default"],
+ adjacentDrugs: ["default"],
+ adjacentDisorders: ["default"],
+ adjacentDrugsAndDisorders: ["default"],
+ drugTarget: ["default"],
+ drug: ["default"],
+ drugTargetAndSeeds: ["default"],
+ drugAndSeeds: ["default"],
+ };
public checkNodeGroupContext(nodeGroupKey) {
- if (nodeGroupKey === 'selectedNode') {
+ if (nodeGroupKey === "selectedNode") {
// selected node is not supposed to appear in legend
return false;
}
@@ -40,16 +39,22 @@ export class NetworkLegendComponent implements OnInit {
}
public checkEdgeGroupContext(edgeGroupKey) {
- return !this.contextEdgeGroupsToDelete[this._context].includes(edgeGroupKey);
+ return !this.contextEdgeGroupsToDelete[this._context].includes(
+ edgeGroupKey
+ );
}
public checkIfEdgeConfigEmpty() {
- return Object.keys(this.config.edgeGroups).some(key => this.checkEdgeGroupContext(key));
+ return Object.keys(this.config.edgeGroups).some((key) =>
+ this.checkEdgeGroupContext(key)
+ );
}
- constructor(public drugstoneConfig: DrugstoneConfigService, public legendService: LegendService, public networkHandler: NetworkHandlerService) { }
-
- ngOnInit(): void {
- }
+ constructor(
+ public drugstoneConfig: DrugstoneConfigService,
+ public legendService: LegendService,
+ public networkHandler: NetworkHandlerService
+ ) {}
+ ngOnInit(): void {}
}
diff --git a/src/app/services/legend-service/legend-service.service.ts b/src/app/services/legend-service/legend-service.service.ts
index a883f0dd..cd651ba9 100644
--- a/src/app/services/legend-service/legend-service.service.ts
+++ b/src/app/services/legend-service/legend-service.service.ts
@@ -11,6 +11,7 @@ export class LegendService {
private default_delete = ['foundNode', 'foundDrug', 'seedNode', 'default', 'defaultDisorder', 'connectorNode'];
private context = [];
+ public networkHasConnector = false;
private contextNodeGroupsToDelete = {
adjacentDrugs: ['foundNode', 'seedNode', 'default', 'defaultDisorder', 'connectorNode'],
@@ -41,6 +42,12 @@ export class LegendService {
const out = [].concat(this.default_delete);
for (const node of this.default_delete) {
let keep = false;
+
+ // delete connectorNodes if network does not contain any
+ if (node === 'connectorNode' && !this.networkHasConnector) {
+ break;
+ }
+
for (const c of this.context) {
if (this.contextNodeGroupsToDelete[c].indexOf(node) === -1) {
keep = true;
diff --git a/src/index.html b/src/index.html
index c25ff979..f21e306c 100644
--- a/src/index.html
+++ b/src/index.html
@@ -115,7 +115,7 @@ menu<br>
<!-- task-id="ks38WxeCSdbXk2cajKACinnUnCHWbf4I" -->
<drugst-one id="netexp1"
groups='{"nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Seed","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Discovered target","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}'
- config='{"customEdges":{"default":true, "selectable":false}, "showAdvAnalysisContent":["drug-search", "enrichment-gprofiler", "enrichment-digest", "search-ndex"],"identifier":"symbol","title":"ROBUST output network", "taskDrugName": "Drug Search", "showLegendNodes": true, "showLegendEdges": true, "showSidebar": "left", "showOverview": true, "legendPos": "left", "legendClass": "legend", "showQuery": true, "showItemSelector": true,"showSimpleAnalysis": false,"showAdvAnalysis": true,"showSelection": true,"showTasks": true,"showNetworkMenu": "right","showLegend": true,"showNetworkMenuButtonExpression": true, "showNetworkMenuButtonScreenshot": true,"showNetworkMenuButtonExportGraphml": true,"showNetworkMenuButtonAdjacentDrugs": true,"showNetworkMenuButtonCenter": true,"showConnectGenes": false,"networkMenuButtonAdjacentDrugsLabel": "Drugs","showNetworkMenuButtonAdjacentDisordersProteins": true,"networkMenuButtonAdjacentDisordersProteinsLabel": "Disorders (protein)","showNetworkMenuButtonAdjacentDisordersDrugs": true,"networkMenuButtonAdjacentDisordersDrugsLabel": "Disorders (drug)","showNetworkMenuButtonAnimation": true,"networkMenuButtonAnimationLabel": "Animation", "autofillEdges": false, "physicsOn": false,"useNedrexLicenced": true,"selfReferences": false, "interactionDrugProtein": "NeDRex", "indicationDrugDisorder": "NeDRex","nodeShadow": true,"edgeShadow": true, "algorithms": {"drug": ["trustrank", "closeness", "degree", "proximity"], "drug-target": ["trustrank", "multisteiner", "keypathwayminer", "degree", "closeness", "betweenness"]}, "associatedProteinDisorder": "NeDRex", "nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Seed","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Discovered target","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}'
+ config='{"customEdges":{"default":true, "selectable":false}, "showAdvAnalysisContent":["drug-search", "drug-target-search", "enrichment-gprofiler", "enrichment-digest", "search-ndex"],"identifier":"symbol","title":"ROBUST output network", "taskDrugName": "Drug Search", "showLegendNodes": true, "showLegendEdges": true, "showSidebar": "left", "showOverview": true, "legendPos": "left", "legendClass": "legend", "showQuery": true, "showItemSelector": true,"showSimpleAnalysis": false,"showAdvAnalysis": true,"showSelection": true,"showTasks": true,"showNetworkMenu": "right","showLegend": true,"showNetworkMenuButtonExpression": true, "showNetworkMenuButtonScreenshot": true,"showNetworkMenuButtonExportGraphml": true,"showNetworkMenuButtonAdjacentDrugs": true,"showNetworkMenuButtonCenter": true,"showConnectGenes": false,"networkMenuButtonAdjacentDrugsLabel": "Drugs","showNetworkMenuButtonAdjacentDisordersProteins": true,"networkMenuButtonAdjacentDisordersProteinsLabel": "Disorders (protein)","showNetworkMenuButtonAdjacentDisordersDrugs": true,"networkMenuButtonAdjacentDisordersDrugsLabel": "Disorders (drug)","showNetworkMenuButtonAnimation": true,"networkMenuButtonAnimationLabel": "Animation", "autofillEdges": false, "physicsOn": false,"useNedrexLicenced": true,"selfReferences": false, "interactionDrugProtein": "NeDRex", "indicationDrugDisorder": "NeDRex","nodeShadow": true,"edgeShadow": true, "algorithms": {"drug": ["trustrank", "closeness", "degree", "proximity"], "drug-target": ["trustrank", "multisteiner", "keypathwayminer", "degree", "closeness", "betweenness"]}, "associatedProteinDisorder": "NeDRex", "nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Seed","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Discovered target","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}'
network='{"nodes": [{"id": "DEFA1", "group": "gene"},{"id": "DEFA1", "group": "gene"}, {"id": "CST6", "group": "gene"}, {"id": "IGFBP2", "group": "gene"}, {"id": "TNFSF8", "group": "gene"}, {"id": "COPRS", "group": "gene"}, {"id": "AGT", "group": "important"}, {"id": "IL6", "group": "important"}, {"id": "A2M", "group": "gene"}, {"id": "NLRP3", "group": "important"}, {"id": "TLR4", "group": "important"}, {"id": "TNFSF9", "group": "gene"}, {"id": "RPL18", "group": "gene"}, {"id": "F5", "group": "gene"}, {"id": "IVL", "group": "gene"}, {"id": "IL6R", "group": "gene"}, {"id": "CPB2", "group": "gene"}, {"id": "CCDC8", "group": "gene"}, {"id": "SERPINB6", "group": "gene"}, {"id": "MBL2", "group": "important"}, {"id": "IL1B", "group": "important"}, {"id": "HIST1H3E", "group": "gene"}, {"id": "IL24", "group": "gene"}, {"id": "GSDMB", "group": "gene"}, {"id": "NOTCH2", "group": "gene"}, {"id": "F2", "group": "important"}, {"id": "CCR5", "group": "important"}, {"id": "SERPINB8", "group": "gene"}, {"id": "KRT1", "group": "gene"}, {"id": "IL1RN", "group": "important"}, {"id": "PLAT", "group": "gene"}, {"id": "URB1", "group": "gene"}, {"id": "FCF1", "group": "gene"}, {"id": "ACE", "group": "important"}, {"id": "THBS3", "group": "gene"}, {"id": "CALML3", "group": "gene"}, {"id": "PSMA5", "group": "gene"}, {"id": "NDUFA3", "group": "gene"}, {"id": "PARK2", "group": "gene"}, {"id": "FANCB", "group": "gene"}, {"id": "SERPINB2", "group": "gene"}, {"id": "KLRG2", "group": "gene"}, {"id": "FAM19A3", "group": "gene"}, {"id": "CRYZL1", "group": "gene"}, {"id": "HEATR1", "group": "gene"}, {"id": "IGHG2", "group": "gene"}, {"id": "C17orf70", "group": "gene"}, {"id": "TINAG", "group": "gene"}, {"id": "RSPRY1", "group": "gene"}, {"id": "TMPRSS11A", "group": "gene"}, {"id": "SLC18A1", "group": "gene"}, {"id": "PSMD1", "group": "gene"}, {"id": "PCDHB15", "group": "gene"}, {"id": "TSR3", "group": "gene"}, {"id": "FGL1", "group": "gene"}, {"id": "C7orf60", "group": "gene"}, {"id": "SSR3", "group": "gene"}, {"id": "REN", "group": "gene"}, {"id": "MYH14", "group": "gene"}, {"id": "TBCK", "group": "gene"}, {"id": "DARS", "group": "gene"}, {"id": "C16orf70", "group": "gene"}, {"id": "DQX1", "group": "gene"}, {"id": "RPL30", "group": "gene"}, {"id": "FBXO30", "group": "gene"}, {"id": "EPPK1", "group": "gene"}, {"id": "LAMA1", "group": "gene"}, {"id": "AP4E1", "group": "gene"}, {"id": "AP4S1", "group": "gene"}, {"id": "HIST1H1B", "group": "gene"}, {"id": "AFP", "group": "gene"}], "edges": [{"from": "DEFA1", "to": "PLAT", "group": "default"}, {"from": "DEFA1", "to": "IGFBP2", "group": "default"}, {"from": "CST6", "to": "FCF1", "group": "default"}, {"from": "CST6", "to": "NOTCH2", "group": "default"}, {"from": "IGFBP2", "to": "GSDMB", "group": "default"}, {"from": "TNFSF8", "to": "F5", "group": "default"}, {"from": "TNFSF8", "to": "TNFSF9", "group": "default"}, {"from": "COPRS", "to": "HIST1H3E", "group": "default"}, {"from": "COPRS", "to": "IL6R", "group": "default"}, {"from": 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"default"}, {"from": "IL1RN", "to": "FCF1", "group": "default"}, {"from": "PLAT", "to": "SERPINB2", "group": "default"}, {"from": "PLAT", "to": "FGL1", "group": "default"}, {"from": "PLAT", "to": "LAMA1", "group": "default"}, {"from": "FCF1", "to": "CALML3", "group": "default"}, {"from": "FCF1", "to": "SERPINB2", "group": "default"}, {"from": "FCF1", "to": "IGHG2", "group": "default"}, {"from": "FCF1", "to": "MYH14", "group": "default"}, {"from": "FCF1", "to": "RPL30", "group": "default"}, {"from": "FCF1", "to": "EPPK1", "group": "default"}, {"from": "THBS3", "to": "NDUFA3", "group": "default"}, {"from": "THBS3", "to": "FANCB", "group": "default"}, {"from": "CALML3", "to": "PARK2", "group": "default"}, {"from": "PSMA5", "to": "PARK2", "group": "default"}, {"from": "PSMA5", "to": "HEATR1", "group": "default"}, {"from": "PSMA5", "to": "PSMD1", "group": "default"}, {"from": "PSMA5", "to": "DARS", "group": "default"}, {"from": "NDUFA3", "to": "SLC18A1", "group": "default"}, {"from": "NDUFA3", "to": "DQX1", "group": "default"}, {"from": "FAM19A3", "to": "CRYZL1", "group": "default"}, {"from": "RSPRY1", "to": "TMPRSS11A", "group": "default"}, {"from": "RSPRY1", "to": "SLC18A1", "group": "default"}, {"from": "PCDHB15", "to": "SSR3", "group": "default"}, {"from": "PCDHB15", "to": "TBCK", "group": "default"}, {"from": "TSR3", "to": "FGL1", "group": "default"}, {"from": "TSR3", "to": "C7orf60", "group": "default"}, {"from": "C7orf60", "to": "REN", "group": "default"}, {"from": "SSR3", "to": "MYH14", "group": "default"}, {"from": "C16orf70", "to": "FBXO30", "group": "default"}, {"from": "DQX1", "to": "FBXO30", "group": "default"}, {"from": "LAMA1", "to": "AP4E1", "group": "default"}, {"from": "AP4E1", "to": "AP4S1", "group": "default"}, {"from": "AP4S1", "to": "AFP", "group": "default"}]}'>
</drugst-one>
--
GitLab