From 446732cf1fb1c2eceed710cf0508147c0ad55c50 Mon Sep 17 00:00:00 2001
From: Michael Hartung <michi@Michaels-MacBook-Pro.local>
Date: Tue, 20 Jul 2021 19:12:56 +0200
Subject: [PATCH] edges in analysis network; handdling of node labels,
replacing by chosen identifier if unset instead of netexId; handling of
multiple ensg numbers for same node missing
---
package-lock.json | 30 +++-
.../analysis-panel.component.html | 13 +-
.../analysis-panel.component.ts | 130 +++++++-----------
.../network-legend.component.ts | 1 +
src/app/interfaces.ts | 32 +----
src/app/main-network.ts | 116 ++++++++--------
.../explorer-page.component.html | 23 ++--
.../explorer-page/explorer-page.component.ts | 22 ++-
8 files changed, 173 insertions(+), 194 deletions(-)
diff --git a/package-lock.json b/package-lock.json
index 4adaa340..590d8325 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -3130,6 +3130,16 @@
"integrity": "sha512-jDctJ/IVQbZoJykoeHbhXpOlNBqGNcwXJKJog42E5HDPUwQTSdjCHdihjj0DlnheQ7blbT6dHOafNAiS8ooQKA==",
"dev": true
},
+ "bindings": {
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
+ "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
+ "dev": true,
+ "optional": true,
+ "requires": {
+ "file-uri-to-path": "1.0.0"
+ }
+ },
"bl": {
"version": "4.1.0",
"resolved": "https://registry.npmjs.org/bl/-/bl-4.1.0.tgz",
@@ -5498,6 +5508,13 @@
"escape-string-regexp": "^1.0.5"
}
},
+ "file-uri-to-path": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
+ "integrity": "sha512-0Zt+s3L7Vf1biwWZ29aARiVYLx7iMGnEUl9x33fbB/j3jR81u/O2LbqK+Bm1CDSNDKVtJ/YjwY7TUd5SkeLQLw==",
+ "dev": true,
+ "optional": true
+ },
"fill-range": {
"version": "7.0.1",
"resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz",
@@ -8277,6 +8294,13 @@
"integrity": "sha512-nnbWWOkoWyUsTjKrhgD0dcz22mdkSnpYqbEjIm2nhwhuxlSkpywJmBo8h0ZqJdkp73mb90SssHkN4rsRaBAfAA==",
"dev": true
},
+ "nan": {
+ "version": "2.14.2",
+ "resolved": "https://registry.npmjs.org/nan/-/nan-2.14.2.tgz",
+ "integrity": "sha512-M2ufzIiINKCuDfBSAUr1vWQ+vuVcA9kqx8JJUsbQi6yf1uGRyb7HfpdfUr5qLXf3B/t8dPvcjhKMmlfnP47EzQ==",
+ "dev": true,
+ "optional": true
+ },
"nanoid": {
"version": "3.1.23",
"resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.23.tgz",
@@ -14048,7 +14072,11 @@
"resolved": "https://registry.npmjs.org/fsevents/-/fsevents-1.2.13.tgz",
"integrity": "sha512-oWb1Z6mkHIskLzEJ/XWX0srkpkTQ7vaopMQkyaEIoq0fmtFVxOthb8cCxeT+p3ynTdkk/RZwbgG4brR5BeWECw==",
"dev": true,
- "optional": true
+ "optional": true,
+ "requires": {
+ "bindings": "^1.5.0",
+ "nan": "^2.12.1"
+ }
},
"glob-parent": {
"version": "3.1.0",
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index a38369d2..313c541f 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -127,7 +127,7 @@
<div class="tab-content" *ngIf="task && task.info.done" [class.is-visible]="tab === 'network'">
<div class="card-image canvas-content" #networkWithLegend>
<div *ngIf="myConfig.showLegend">
- <app-network-legend [config]="myConfig" [analysis]="false"></app-network-legend>
+ <app-network-legend [config]="myConfig" [analysis]="true"></app-network-legend>
</div>
<div class="fullheight center image1" #network>
<button class="button is-loading center">Loading</button>
@@ -180,7 +180,9 @@
<div class="dropdown-trigger">
<button (click)="expressionExpanded=!expressionExpanded"
class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
- aria-haspopup="true" aria-controls="dropdown-menu" [ngClass]="{'button-small':smallStyle}">
+ aria-haspopup="true" aria-controls="dropdown-menu" [ngClass]="{'button-small':smallStyle}"
+ pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
+ >
<div [ngClass]="{'text-small':smallStyle}">
<span *ngIf="!selectedTissue">Tissue</span>
<span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
@@ -212,9 +214,10 @@
</div>
<app-toggle *ngIf="task.info.target === 'drug-target'" class="footer-buttons" textOn="Drugs On" textOff="Off"
- tooltipOn="Display drugs in the network" tooltipOff="Hide drugs in the network"
- [smallStyle]="smallStyle"
- [value]="showDrugs" (valueChange)="toggleDrugs($event)"></app-toggle>
+ tooltipOn="Display adjacent drugs ON."
+ tooltipOff="Display adjacent drugs OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
<app-toggle class="footer-buttons" textOn="Animation On" textOff="Off"
tooltipOn="Enable the network animation."
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index a62795cf..c51e633d 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -9,18 +9,15 @@ import {
SimpleChanges,
ViewChild,
} from '@angular/core';
-import {HttpClient, HttpErrorResponse} from '@angular/common/http';
+import {HttpClient} from '@angular/common/http';
import {environment} from '../../../environments/environment';
import {algorithmNames, AnalysisService} from '../../services/analysis/analysis.service';
import {
Drug,
EdgeType,
- getNodeIdsFromPDI,
- getNodeIdsFromPPI,
+ getDrugNodeId,
getProteinNodeId,
- getWrapperFromDrug,
getWrapperFromNode,
- getWrapperFromProtein,
Node,
Task,
Tissue,
@@ -31,6 +28,7 @@ import {toast} from 'bulma-toast';
import {NetworkSettings} from '../../network-settings';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
import {defaultConfig, IConfig} from 'src/app/config';
+import { mapCustomEdge, mapCustomNode } from 'src/app/main-network';
declare var vis: any;
@@ -85,6 +83,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public tab: 'meta' | 'network' | 'table' = 'table';
public physicsEnabled = true;
+ public adjacentDrugs = false;
+ public adjacentDrugList: Node[] = [];
+ public adjacentDrugEdgesList: Node[] = [];
+
private proteins: any;
public effects: any;
@@ -427,6 +429,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
*/
public createNetwork(result: any): { edges: any[], nodes: any[] } {
const config = result.parameters.config;
+ this.myConfig = config;
+
+ console.log(config)
+ console.log('config')
+
+ const identifier = this.myConfig.identifier;
// add drugGroup and foundNodesGroup for added nodes
// these groups can be overwritten by the user
@@ -443,30 +451,36 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const isSeed = attributes.isSeed || {};
const scores = attributes.scores || {};
const details = attributes.details || {};
- const wrappers: { [key: string]: Wrapper } = {};
for (const node of network.nodes) {
// convert id to netex Id if exists
const nodeDetails = details[node];
+
+ nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.netexId;
if (nodeDetails.netexId && nodeDetails.netexId.startsWith('p')) {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
+ nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'foundNode';
+ nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
this.proteins.push(nodeDetails);
- wrappers[node] = getWrapperFromProtein(nodeDetails as Node);
} else if (nodeDetails.netexId && nodeDetails.netexId.startsWith('d')) {
// node is drug, was found during analysis
- wrappers[node] = getWrapperFromDrug(nodeDetails as Drug);
+ nodeDetails.type = 'Drug';
+ nodeDetails.group = 'foundDrug';
} else {
// node is custom input from user, could not be mapped to backend protein
- wrappers[node] = getWrapperFromNode(nodeDetails as Node);
+ nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'default';
+ nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier]
}
// IMPORTANT we set seeds to "selected" and not to seeds. The user should be inspired to run
// 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(wrappers[node].data as Node, config, false, isSeed[node], 1))
+ nodes.push(NetworkSettings.getNodeStyle(nodeDetails as Node, config, false, isSeed[node], 1))
}
+ console.log('nodes')
+ console.log(nodes)
for (const edge of network.edges) {
- edges.push(this.mapEdge(edge, this.inferEdgeGroup(edge), wrappers));
+ edges.push(mapCustomEdge(edge, this.myConfig));
}
return {
nodes,
@@ -474,80 +488,28 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
};
}
- private mapEdge(edge: any, type: 'protein-protein' | 'protein-drug', wrappers?: { [key: string]: Wrapper }): any {
- let edgeColor;
- if (type === 'protein-protein') {
- edgeColor = {
- color: NetworkSettings.getColor('edgeGeneGene'),
- highlight: NetworkSettings.getColor('edgeGeneGeneHighlight'),
- };
- const {from, to} = getNodeIdsFromPPI(edge, wrappers);
- return {
- from, to,
- color: edgeColor,
- };
- } else if (type === 'protein-drug') {
- edgeColor = {
- color: NetworkSettings.getColor('edgeHostDrug'),
- highlight: NetworkSettings.getColor('edgeHostDrugHighlight'),
- };
- const {from, to} = getNodeIdsFromPDI(edge);
- return {
- from, to,
- color: edgeColor,
- };
- }
- }
-
- public async toggleDrugs(bool: boolean) {
- this.showDrugs = bool;
- this.nodeData.nodes.remove(this.drugNodes);
- this.nodeData.edges.remove(this.drugEdges);
- this.drugNodes = [];
- this.drugEdges = [];
- if (this.showDrugs) {
- const result = await this.http.get<any>(
- `${environment.backend}drug_interactions/?token=${this.token}`).toPromise().catch(
- (err: HttpErrorResponse) => {
- // simple logging, but you can do a lot more, see below
- toast({
- message: 'An error occured while fetching the drugs.',
- duration: 5000,
- dismissible: true,
- pauseOnHover: true,
- type: 'is-danger',
- position: 'top-center',
- animate: {in: 'fadeIn', out: 'fadeOut'}
- });
- this.showDrugs = false;
- return;
- });
-
- const drugs = result.drugs;
- const edges = result.edges;
-
- if (drugs.length === 0) {
- toast({
- message: 'No drugs found.',
- duration: 5000,
- dismissible: true,
- pauseOnHover: true,
- type: 'is-warning',
- position: 'top-center',
- animate: {in: 'fadeIn', out: 'fadeOut'}
- });
- } else {
- // for (const drug of drugs) {
- // this.drugNodes.push(this.mapNode(config, 'drug', drug, false, null));
- // }
- for (const interaction of edges) {
- const edge = {from: interaction.uniprotAc, to: interaction.drugId};
- this.drugEdges.push(this.mapEdge(edge, 'protein-drug'));
- }
- this.nodeData.nodes.add(Array.from(this.drugNodes.values()));
- this.nodeData.edges.add(Array.from(this.drugEdges.values()));
- }
+ public updateAdjacentDrugs(bool: boolean) {
+ this.adjacentDrugs = bool;
+ if (this.adjacentDrugs) {
+ this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
+ for (const interaction of response.pdis) {
+ const edge = {from: interaction.protein, to: interaction.drug};
+ this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ }
+ for (const drug of response.drugs) {
+ drug.group = 'foundDrug';
+ drug.id = getDrugNodeId(drug)
+ this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
+ }
+ this.nodeData.nodes.add(this.adjacentDrugList);
+ this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ })
+ } else {
+ this.nodeData.nodes.remove(this.adjacentDrugList);
+ this.nodeData.edges.remove(this.adjacentDrugEdgesList);
+ this.adjacentDrugList = [];
+ this.adjacentDrugEdgesList = [];
}
}
diff --git a/src/app/components/network-legend/network-legend.component.ts b/src/app/components/network-legend/network-legend.component.ts
index 64984b1a..10bdb07d 100644
--- a/src/app/components/network-legend/network-legend.component.ts
+++ b/src/app/components/network-legend/network-legend.component.ts
@@ -13,6 +13,7 @@ export class NetworkLegendComponent implements OnInit {
@Input() set config(value: IConfig) {
// copy to not override user config
value = JSON.parse(JSON.stringify(value));
+ // remove selected node group since it is just a border
delete value.nodeGroups.selectedNode;
if (!this.analysis) {
// do not show the analysis-groups in the explorer network
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 69fcc9a3..f7c46aa3 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -110,10 +110,6 @@ export function getDrugNodeId(drug: Drug) {
return drug.netexId
}
-export function getDrugBackendId(drug: Drug) {
- return drug.netexId;
-}
-
export function getNodeId(node: Node) {
/**
* Returns backend_id of Gene object
@@ -130,7 +126,7 @@ export function getNetworkId(node: Node) {
/**
* Returns ID of a network node
*/
- return node.id
+ return node.netexId
}
export function getId(gene: Node) {
@@ -140,19 +136,6 @@ export function getId(gene: Node) {
return `${gene.id}`;
}
-export function getWrapperFromProtein(gene: Node): Wrapper {
- /**
- * Constructs wrapper interface for gene
- */
- // if node does not have property group, it was found by the analysis
- gene.group = gene.group ? gene.group : 'foundNode';
- gene.label = gene.label ? gene.label : gene.id
- return {
- id: getNetworkId(gene),
- data: gene,
- };
-}
-
export function getWrapperFromNode(gene: Node): Wrapper {
/**
* Constructs wrapper interface for gene
@@ -161,22 +144,11 @@ export function getWrapperFromNode(gene: Node): Wrapper {
gene.group = gene.group ? gene.group : 'default';
gene.label = gene.label ? gene.label : gene.id
return {
- id: getNetworkId(gene),
+ id: gene.id,
data: gene,
};
}
-
-export function getWrapperFromDrug(drug: Drug): Wrapper {
- // set type and group
- drug.type = 'Drug';
- drug.group = 'foundDrug';
- return {
- id: getDrugNodeId(drug),
- data: drug,
- };
-}
-
export type EdgeType = 'protein-protein' | 'protein-drug';
export interface Wrapper {
diff --git a/src/app/main-network.ts b/src/app/main-network.ts
index 052d040b..c66def70 100644
--- a/src/app/main-network.ts
+++ b/src/app/main-network.ts
@@ -43,71 +43,16 @@ export class ProteinNetwork {
});
}
- /** Maps user input node to network node object
- * If user input node has no group, fall back to default
- * If user input node has group that is not defined, throw error
- *
- * @param customNode
- * @param config
- * @returns
- */
- public mapCustomNode(customNode: any, config: IConfig): Node {
- let node;
- if (customNode.group === undefined) {
- // fallback to default node
- node = JSON.parse(JSON.stringify(defaultConfig.nodeGroups.default));
- node.group = 'default'
- } else {
- if (config.nodeGroups[customNode.group] === undefined) {
- throw `Node with id ${customNode.id} has undefined node group ${customNode.group}.`
- }
- // copy
- node = JSON.parse(JSON.stringify(config.nodeGroups[customNode.group]));
- }
- // update the node with custom node properties, including values fetched from backend
- node = merge(node, customNode)
- // label is only used for network visualization
- node.label = customNode.label ? customNode.label : customNode.id;
- return node;
- }
-
- /** Maps user input edge to network edge object
- * If user input edge has no group, fall back to default
- * If user input edge has group that is not defined, throw error
- *
- * @param customEdge
- * @param config
- * @returns
- */
- public mapCustomEdge(customEdge: NodeInteraction, config: IConfig): any {
- let edge;
- if (customEdge.group === undefined) {
- // fallback to default node
- edge = JSON.parse(JSON.stringify(defaultConfig.edgeGroups.default));
- } else {
- if (config.edgeGroups[customEdge.group] === undefined) {
- throw `Edge "from ${customEdge.from}" - "to ${customEdge.to}" has undefined edge group ${customEdge.group}.`
- }
- // copy
- edge = JSON.parse(JSON.stringify(config.edgeGroups[customEdge.group]));
- }
- edge = {
- ...edge,
- ...customEdge
- }
- return edge;
- }
-
public mapDataToNetworkInput(config: IConfig): { nodes: Node[], edges: any[]; } {
const nodes = [];
const edges = [];
for (const protein of this.proteins) {
- nodes.push(this.mapCustomNode(protein, config));
+ nodes.push(mapCustomNode(protein, config));
}
for (const edge of this.edges) {
- edges.push(this.mapCustomEdge(edge, config));
+ edges.push(mapCustomEdge(edge, config));
}
return {
@@ -117,3 +62,60 @@ export class ProteinNetwork {
}
}
+
+/** Maps user input node to network node object
+ * If user input node has no group, fall back to default
+ * If user input node has group that is not defined, throw error
+ *
+ * @param customNode
+ * @param config
+ * @returns
+ */
+ export function mapCustomNode(customNode: any, config: IConfig): Node {
+ let node;
+ if (customNode.group === undefined) {
+ // fallback to default node
+ node = JSON.parse(JSON.stringify(defaultConfig.nodeGroups.default));
+ node.group = 'default';
+ } else {
+ if (config.nodeGroups[customNode.group] === undefined) {
+ throw `Node with id ${customNode.id} has undefined node group ${customNode.group}.`
+ }
+ // copy
+ node = JSON.parse(JSON.stringify(config.nodeGroups[customNode.group]));
+ }
+ // update the node with custom node properties, including values fetched from backend
+ node = merge(node, customNode)
+ // label is only used for network visualization
+ node.label = customNode.label ? customNode.label : customNode.id;
+ return node;
+}
+
+/** Maps user input edge to network edge object
+ * If user input edge has no group, fall back to default
+ * If user input edge has group that is not defined, throw error
+ *
+ * @param customEdge
+ * @param config
+ * @returns
+ */
+export function mapCustomEdge(customEdge: NodeInteraction, config: IConfig): any {
+ let edge;
+ if (customEdge.group === undefined) {
+ // fallback to default node
+ edge = JSON.parse(JSON.stringify(defaultConfig.edgeGroups.default));
+ } else {
+ if (config.edgeGroups[customEdge.group] === undefined) {
+ throw `Edge "from ${customEdge.from}" - "to ${customEdge.to}" has undefined edge group ${customEdge.group}.`
+ }
+ // copy
+ edge = JSON.parse(JSON.stringify(config.edgeGroups[customEdge.group]));
+ }
+ edge = {
+ ...edge,
+ ...customEdge
+ }
+ console.log('edge')
+ console.log(edge)
+ return edge;
+}
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 9ec8e526..87baa8c7 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -146,6 +146,7 @@
<ng-container *ngIf="myConfig.showFooterButtonExpression">
<div class="footer-buttons dropdown is-up explorer-footer-element" [class.is-active]="expressionExpanded">
+
<div class="dropdown-trigger">
<button (click)="expressionExpanded=!expressionExpanded"
class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
@@ -182,17 +183,17 @@
</div>
</ng-container>
- <app-toggle class="footer-buttons" textOn="Drugs On" textOff="Off"
- tooltipOn="Display adjacent drugs ON."
- tooltipOff="Display adjacent drugs OFF."
- [smallStyle]="smallStyle"
- [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
-
- <app-toggle class="footer-buttons explorer-footer-element" textOn="Animation On" textOff="Off"
- tooltipOn="Enable the network animation."
- tooltipOff="Disable the network animation and freeze nodes."
- [smallStyle]="smallStyle"
- [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
+ <app-toggle class="footer-buttons" textOn="Drugs On" textOff="Off"
+ tooltipOn="Display adjacent drugs ON."
+ tooltipOff="Display adjacent drugs OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
+
+ <app-toggle class="footer-buttons explorer-footer-element" textOn="Animation On" textOff="Off"
+ tooltipOn="Enable the network animation."
+ tooltipOff="Disable the network animation and freeze nodes."
+ [smallStyle]="smallStyle"
+ [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
</footer>
</div>
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index cd2a64d4..c5d09b1a 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -15,7 +15,7 @@ import {
getDrugNodeId,
Drug
} from '../../interfaces';
-import {ProteinNetwork} from '../../main-network';
+import {mapCustomEdge, mapCustomNode, ProteinNetwork} from '../../main-network';
import {AnalysisService} from '../../services/analysis/analysis.service';
import {OmnipathControllerService} from '../../services/omnipath-controller/omnipath-controller.service';
import domtoimage from 'dom-to-image';
@@ -269,10 +269,20 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (network.nodes.length) {
network.nodes = await this.netex.mapNodes(network.nodes, this.myConfig.identifier);
}
- // use netexIds where posssible
+ // at this point, we have nodes synched with the backend
+ // use netexIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
- network.nodes.forEach(node => {
- nodeIdMap[node.id] = node.netexId ? node.netexId : node.id
+ const seenNodeIds = new Set();
+ network.nodes.forEach((node, index, object) => {
+ if (seenNodeIds.has(node.id)) {
+ // remove duplicate ensg nodes, TODO is there a better way to do this?
+ object.splice(index, 1);
+ return;
+ } else {
+ seenNodeIds.add(node.id);
+ }
+ nodeIdMap[node.id] = node.netexId ? node.netexId : node.id;
+ node.label = node.label ? node.label : node.id;
node.id = nodeIdMap[node.id];
});
// adjust edge labels accordingly
@@ -425,12 +435,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
for (const interaction of response.pdis) {
const edge = {from: interaction.protein, to: interaction.drug};
- this.adjacentDrugEdgesList.push(this.proteinData.mapCustomEdge(edge, this.myConfig));
+ this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
}
for (const drug of response.drugs) {
drug.group = 'foundDrug';
drug.id = getDrugNodeId(drug)
- this.adjacentDrugList.push(this.proteinData.mapCustomNode(drug, this.myConfig))
+ this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
}
this.nodeData.nodes.add(this.adjacentDrugList);
this.nodeData.edges.add(this.adjacentDrugEdgesList);
--
GitLab