From 340e9c0821dcb976b993d469cd9cc5b43b84b0a2 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Wed, 2 Nov 2022 09:27:08 +0100
Subject: [PATCH] added config for activating adjacent drugs and disorders
---
.../analysis-panel.component.ts | 1 +
.../components/network/network.component.ts | 167 ++++++++++--------
src/app/config.ts | 7 +-
.../explorer-page/explorer-page.component.ts | 1 +
.../network-handler.service.ts | 19 +-
src/index.html | 2 +-
6 files changed, 117 insertions(+), 80 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 16c484db..be1a6a75 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -204,6 +204,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (!this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
+ this.networkHandler.updateAdjacentNodes();
});
this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
this.tableDrugs.forEach((r) => {
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 7366ff22..d13a9c9d 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -21,7 +21,7 @@ import {NetworkSettings} from 'src/app/network-settings';
import {pieChartContextRenderer} from 'src/app/utils';
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 {LoadingScreenService} from 'src/app/services/loading-screen/loading-screen.service';
@Component({
@@ -81,7 +81,7 @@ export class NetworkComponent implements OnInit {
public nodeRenderer = null;
- public loading = false
+ public loading = false;
constructor(
public configService: DrugstoneConfigService,
@@ -91,8 +91,8 @@ export class NetworkComponent implements OnInit {
public drugstoneConfig: DrugstoneConfigService,
public netex: NetexControllerService,
public omnipath: OmnipathControllerService,
- public loadingScreen: LoadingScreenService)
- {}
+ public loadingScreen: LoadingScreenService) {
+ }
ngOnInit(): void {
this.networkHandler.networks[this.networkType] = this;
@@ -116,15 +116,16 @@ export class NetworkComponent implements OnInit {
updateQueryItems() {
this.queryItems = [];
- if (this.currentViewNodes)
+ if (this.currentViewNodes) {
this.currentViewNodes.forEach((protein) => {
this.queryItems.push(getWrapperFromNode(protein));
});
+ }
}
public saveAddNodes(nodeList: Node[]) {
const existing = this.nodeData.nodes.get().map(n => n.id);
- const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1)
+ const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1);
this.nodeData.nodes.add(toAdd);
}
@@ -132,31 +133,33 @@ export class NetworkComponent implements OnInit {
this.loadingScreen.stateUpdate(true);
this.adjacentDisordersProtein = bool;
if (this.adjacentDisordersProtein) {
- this.legendService.add_to_context('adjacentDisorders')
+ this.legendService.add_to_context('adjacentDisorders');
this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'proteins', this.drugstoneConfig.config.associatedProteinDisorder, this.drugstoneConfig.config.licensedDatasets).subscribe(response => {
- const proteinMap = this.getProteinMap()
- const addedEdge = {}
+ const proteinMap = this.getProteinMap();
+ const addedEdge = {};
for (const interaction of response.edges) {
- const edge = mapCustomEdge({from: interaction.protein, to: interaction.disorder}, this.drugstoneConfig.config)
+ const edge = mapCustomEdge({from: interaction.protein, to: interaction.disorder}, this.drugstoneConfig.config);
if (proteinMap[edge.from]) {
proteinMap[edge.from].forEach(from => {
- if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1)
- return
- const e = JSON.parse(JSON.stringify(edge))
- e.from = from
- e.to = edge.to
+ if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
+ return;
+ }
+ const e = JSON.parse(JSON.stringify(edge));
+ e.from = from;
+ e.to = edge.to;
this.adjacentProteinDisorderEdgesList.push(e);
- if (!addedEdge[from])
- addedEdge[from] = [edge.to]
- else
- addedEdge[from].push(edge.to)
- })
+ if (!addedEdge[from]) {
+ addedEdge[from] = [edge.to];
+ } else {
+ addedEdge[from].push(edge.to);
+ }
+ });
}
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
disorder.id = disorder.drugstoneId;
- this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig()))
+ this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig()));
}
this.saveAddNodes(this.adjacentProteinDisorderList);
this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
@@ -197,8 +200,9 @@ export class NetworkComponent implements OnInit {
this.loadingScreen.stateUpdate(false);
});
} else {
- if (!this.adjacentDisordersProtein)
+ if (!this.adjacentDisordersProtein) {
this.legendService.remove_from_context('adjacentDisorders');
+ }
this.saveRemoveDisorders(this.adjacentDrugDisorderList);
this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
this.adjacentDrugDisorderList = [];
@@ -209,68 +213,73 @@ export class NetworkComponent implements OnInit {
}
public getProteinMap() {
- const proteinMap = {}
+ const proteinMap = {};
this.nodeData.nodes.get().forEach(n => {
if (n.drugstoneType === 'protein') {
n.drugstoneId.forEach(id => {
if (typeof id === 'string') {
- if (proteinMap[id])
- proteinMap[id].push(n.id)
- else
+ if (proteinMap[id]) {
+ proteinMap[id].push(n.id);
+ } else {
proteinMap[id] = [n.id];
+ }
} else {
n.id.forEach(single_id => {
- if (proteinMap[single_id])
- proteinMap[single_id].push(n.id)
- else
+ if (proteinMap[single_id]) {
+ proteinMap[single_id].push(n.id);
+ } else {
proteinMap[single_id] = [n.id];
- })
+ }
+ });
}
});
}
});
- return proteinMap
+ return proteinMap;
}
public updateAdjacentDrugs(bool: boolean) {
this.loadingScreen.stateUpdate(true);
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
- this.legendService.add_to_context("adjacentDrugs")
- const addedEdge = {}
- const proteinMap = this.getProteinMap()
+ this.legendService.add_to_context('adjacentDrugs');
+ const addedEdge = {};
+ const proteinMap = this.getProteinMap();
this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licensedDatasets, this.nodeData.nodes.get()).subscribe(response => {
const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
for (const interaction of response.pdis) {
- const edge = mapCustomEdge({from: interaction.protein, to: interaction.drug}, this.drugstoneConfig.currentConfig())
+ const edge = mapCustomEdge({from: interaction.protein, to: interaction.drug}, this.drugstoneConfig.currentConfig());
if (proteinMap[edge.from]) {
proteinMap[edge.from].forEach(from => {
- if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1)
- return
- const e = JSON.parse(JSON.stringify(edge))
- e.from = from
- e.to = edge.to
+ if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
+ return;
+ }
+ const e = JSON.parse(JSON.stringify(edge));
+ e.from = from;
+ e.to = edge.to;
this.adjacentDrugEdgesList.push(e);
- if (!addedEdge[from])
- addedEdge[from] = [edge.to]
- else
- addedEdge[from].push(edge.to)
- })
+ if (!addedEdge[from]) {
+ addedEdge[from] = [edge.to];
+ } else {
+ addedEdge[from].push(edge.to);
+ }
+ });
}
}
for (const drug of response.drugs) {
drug.group = 'foundDrug';
drug.id = getDrugNodeId(drug);
- if (existingDrugIDs.indexOf(drug.drugstoneId) === -1) {
- this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig()))
+ if (!existingDrugIDs.includes(drug.drugstoneId)) {
+ existingDrugIDs.push(drug.drugstoneId);
+ this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig()));
}
}
this.nodeData.nodes.add(this.adjacentDrugList);
this.nodeData.edges.add(this.adjacentDrugEdgesList);
this.updateQueryItems();
this.loadingScreen.stateUpdate(false);
- })
+ });
} else {
// remove adjacent drugs, make sure that also drug associated disorders are removed
if (this.adjacentDisordersDrug) {
@@ -290,13 +299,13 @@ export class NetworkComponent implements OnInit {
}
public saveRemoveDisorders(nodeList: Node[]) {
- const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
- if (other == null)
+ const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList;
+ if (other == null) {
this.nodeData.nodes.remove(nodeList);
- else {
+ } else {
const otherIds = other.map(d => d.id);
- const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1)
- this.nodeData.nodes.remove(rest)
+ const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1);
+ this.nodeData.nodes.remove(rest);
}
}
@@ -367,7 +376,7 @@ export class NetworkComponent implements OnInit {
this.nodeRenderer = null;
const updatedNodes = [];
// for (const item of this.proteins) {
- const proteins = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'protein')
+ const proteins = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'protein');
for (const node of proteins) {
const pos = this.networkInternal.getPositions([node.id]);
node.x = pos[node.id].x;
@@ -421,31 +430,33 @@ export class NetworkComponent implements OnInit {
const updatedNodes = [];
this.nodeRenderer = pieChartContextRenderer;
// mapping from netex IDs to network IDs, TODO check if this step is necessary
- const networkIdMapping = {}
+ const networkIdMapping = {};
this.nodeData.nodes.get().forEach(element => {
if (element.drugstoneType === 'protein') {
element.drugstoneId.forEach(id => {
- if (networkIdMapping[id])
+ if (networkIdMapping[id]) {
networkIdMapping[id].push(element.id);
- else
- networkIdMapping[id] = [element.id]
+ } else {
+ networkIdMapping[id] = [element.id];
+ }
});
}
});
const maxExpr = Math.max(...Object.values(this.expressionMap));
- const exprMap = {}
+ const exprMap = {};
for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
networkIdMapping[drugstoneId].forEach(networkId => {
- if (!exprMap[networkId])
- exprMap[networkId] = [expressionlvl]
- else
- exprMap[networkId].push(expressionlvl)
- })
+ if (!exprMap[networkId]) {
+ exprMap[networkId] = [expressionlvl];
+ } else {
+ exprMap[networkId].push(expressionlvl);
+ }
+ });
}
- this.expressionMap = {}
+ this.expressionMap = {};
Object.keys(exprMap).forEach(networkId => {
const expressionlvl = exprMap[networkId] ? exprMap[networkId].reduce((a, b) => a + b) / exprMap[networkId].length : null;
- this.expressionMap[networkId] = expressionlvl
+ this.expressionMap[networkId] = expressionlvl;
const node = this.nodeData.nodes.get(networkId);
if (node === null) {
return;
@@ -468,20 +479,23 @@ export class NetworkComponent implements OnInit {
node.shape = 'custom';
node.ctxRenderer = pieChartContextRenderer;
updatedNodes.push(node);
- })
+ });
this.nodeData.nodes.update(updatedNodes);
this.loadingScreen.stateUpdate(false);
}
- )
+ );
}
this.currentViewSelectedTissue = this.selectedTissue;
}
public hasDrugsLoaded(): boolean {
- if (this.nodeData && this.nodeData.nodes)
- for (const node of this.nodeData.nodes.get())
- if (node.drugstoneType && node.drugstoneId === 'drug')
+ if (this.nodeData && this.nodeData.nodes) {
+ for (const node of this.nodeData.nodes.get()) {
+ if (node.drugstoneType && node.drugstoneId === 'drug') {
return true;
+ }
+ }
+ }
return false;
}
@@ -497,10 +511,11 @@ export class NetworkComponent implements OnInit {
this.loadingScreen.stateUpdate(true);
this.highlightSeeds = bool;
const updatedNodes = [];
- if (this.highlightSeeds)
- this.legendService.add_to_context('seeds')
- else
- this.legendService.remove_from_context('seeds')
+ if (this.highlightSeeds) {
+ this.legendService.add_to_context('seeds');
+ } else {
+ this.legendService.remove_from_context('seeds');
+ }
for (const node of this.nodeData.nodes.get().filter(n => n.drugstoneType === 'protein')) {
if (node.drugstoneId === undefined) {
// nodes that are not mapped to backend remain untouched
@@ -510,7 +525,7 @@ export class NetworkComponent implements OnInit {
if (!node) {
continue;
}
- console.log(node)
+ console.log(node);
const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([node.id]);
node.x = pos[node.id].x;
node.y = pos[node.id].y;
diff --git a/src/app/config.ts b/src/app/config.ts
index 31da31f9..21914c8c 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -60,11 +60,14 @@ export interface IConfig {
showNetworkMenuButtonScreenshot: boolean;
showNetworkMenuButtonExportGraphml: boolean;
showNetworkMenuButtonAdjacentDrugs: boolean;
+ activateNetworkMenuButtonAdjacentDrugs: boolean;
showNetworkMenuButtonCenter: boolean;
showConnectGenes: boolean;
networkMenuButtonAdjacentDrugsLabel: string;
showNetworkMenuButtonAdjacentDisordersProteins: boolean;
+ activateNetworkMenuButtonAdjacentDisorders: boolean;
networkMenuButtonAdjacentDisordersProteinsLabel: string;
+ activateNetworkMenuButtonAdjacentDisorderDrugs: boolean;
showNetworkMenuButtonAdjacentDisordersDrugs: boolean;
networkMenuButtonAdjacentDisordersDrugsLabel: string;
showNetworkMenuButtonAnimation: boolean;
@@ -155,10 +158,12 @@ export const defaultConfig: IConfig = {
showNetworkMenuButtonScreenshot: true,
showNetworkMenuButtonExportGraphml: true,
showNetworkMenuButtonAdjacentDrugs: true,
+ activateNetworkMenuButtonAdjacentDrugs: false,
showNetworkMenuButtonCenter: true,
showNetworkMenuButtonAnimation: true,
-
+ activateNetworkMenuButtonAdjacentDisorders: false,
showNetworkMenuButtonAdjacentDisordersProteins: true,
+ activateNetworkMenuButtonAdjacentDisorderDrugs: false,
showNetworkMenuButtonAdjacentDisordersDrugs: true,
showConnectGenes: true,
networkMenuButtonAdjacentDrugsLabel: 'Drugs',
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index ab2348c0..9fb7a0fc 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -228,6 +228,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(true);
}
+ this.networkHandler.updateAdjacentNodes();
});
}
}
diff --git a/src/app/services/network-handler/network-handler.service.ts b/src/app/services/network-handler/network-handler.service.ts
index d251fbaa..e422a0b9 100644
--- a/src/app/services/network-handler/network-handler.service.ts
+++ b/src/app/services/network-handler/network-handler.service.ts
@@ -6,8 +6,8 @@ import {AnalysisService} from '../analysis/analysis.service';
import {DrugstoneConfigService} from '../drugstone-config/drugstone-config.service';
import {NetexControllerService} from '../netex-controller/netex-controller.service';
import {OmnipathControllerService} from '../omnipath-controller/omnipath-controller.service';
-import {LegendService} from "../legend-service/legend-service.service";
-import { LoadingScreenService } from '../loading-screen/loading-screen.service';
+import {LegendService} from '../legend-service/legend-service.service';
+import {LoadingScreenService} from '../loading-screen/loading-screen.service';
@Injectable({
providedIn: 'root'
@@ -34,4 +34,19 @@ export class NetworkHandlerService {
get getChange$() {
return this.change.asObservable();
}
+
+ async updateAdjacentNodes() {
+ if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDrugs) {
+ this.activeNetwork.adjacentDrugs = true;
+ await this.activeNetwork.updateAdjacentDrugs(true);
+ }
+ if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDisorders) {
+ this.activeNetwork.adjacentDisordersProtein = true;
+ await this.activeNetwork.updateAdjacentProteinDisorders(true);
+ }
+ if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDisorderDrugs) {
+ this.activeNetwork.adjacentDisordersDrug = true;
+ await this.activeNetwork.updateAdjacentDrugDisorders(true);
+ }
+ }
}
diff --git a/src/index.html b/src/index.html
index 4e5a70b5..e7425fab 100644
--- a/src/index.html
+++ b/src/index.html
@@ -97,7 +97,7 @@
<drugst-one id="tatata"
groups= '{ "nodeGroups" : { "selectedNode": { "borderWidth": 3,"borderWidthSelected": 4,"color": { "border": "#ffffff","highlight": {"border": "#ffffff"}},"font": { "color": "#F8981","size": 14 }},"Protein":{"shape":"circle","groupName":"Protein","type":"Protein","color":"#172b4d","font":{"color":"#ffffff"}}}}'
- config='{ "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": true, "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", "expandNetworkMenu": true}'
+ config='{ "activateNetworkMenuButtonAdjacentDrugs": true,"activateNetworkMenuButtonAdjacentDisorders": true, "activateNetworkMenuButtonAdjacentDisorderDrugs": true, "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": true, "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", "expandNetworkMenu": true}'
network='{"nodes": [{"id":"PSEN1","group":"Protein","label":"PSEN1"},{"id":"PSEN2","group":"Protein","label":"PSEN2"},{"id":"APP","group":"Protein","label":"APP"},{"id":"APOE","group":"Protein","label":"APOE"},{"id":"RNF32","group":"Protein","label":"RNF32"},{"id":"STX5","group":"Protein","label":"STX5"},{"id":"TRAF3IP1","group":"Protein","label":"TRAF3IP1"},{"id":"PHB1","group":"Protein","label":"PHB1"},{"id":"MAPT","group":"Protein","label":"MAPT"},{"id":"ESR1","group":"Protein","label":"ESR1"},{"id":"IRF3","group":"Protein","label":"IRF3"},{"id":"DYNC1H1","group":"Protein","label":"DYNC1H1"},{"id":"CUL3","group":"Protein","label":"CUL3"},{"id":"HMGB1","group":"Protein","label":"HMGB1"},{"id":"DNAJC7","group":"Protein","label":"DNAJC7"},{"id":"NEFM","group":"Protein","label":"NEFM"},{"id":"DISC1","group":"Protein","label":"DISC1"},{"id":"PPP5C","group":"Protein","label":"PPP5C"},{"id":"CTNNB1","group":"Protein","label":"CTNNB1"},{"id":"KRAS","group":"Protein","label":"KRAS"}]}'
></drugst-one>
--
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