diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 26c8b639ee101f4ce4a67a9fe592531a1678540a..a3ba26f0942cccf04f104548175bcb0031295787 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -33,6 +33,7 @@ import {LegendService} from 'src/app/services/legend-service/legend-service.serv
import {LoadingScreenService} from 'src/app/services/loading-screen/loading-screen.service';
import {version} from '../../../version';
import {downloadCSV} from 'src/app/utils';
+import {Observable} from 'rxjs';
declare var vis: any;
@@ -101,6 +102,7 @@ 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) {
try {
this.versionString = version;
@@ -113,6 +115,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
ngAfterViewInit() {
this.networkHandler.setActiveNetwork('analysis');
+ this.networkHandler.activeNetwork.subscribeSelection(() => {
+ this.refresh();
+ }
+ );
}
async ngOnChanges(changes: SimpleChanges) {
@@ -127,7 +133,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.resetEmitter.emit(true);
}
- private setNetworkListeners(){
+ 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) {
@@ -460,7 +466,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
});
});
}).then(nodes => {
-
this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
@@ -493,6 +498,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.setNetworkListeners();
this.emitVisibleItems(true);
}).then(() => {
+ this.loadingScreen.stateUpdate(false);
if (!['quick', 'super', 'connect', 'connectSelected'].includes(this.task.info.algorithm)) {
return;
}
@@ -501,7 +507,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
});
}).catch(console.error);
});
- this.loadingScreen.stateUpdate(false);
});
}
}
@@ -614,7 +619,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// add drugGroup and foundNodesGroup for added nodes
// these groups can be overwritten by the user
- const nodes = [];
+ let nodes = [];
let edges = [];
const attributes = result.nodeAttributes || {};
@@ -648,6 +653,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// node is drug, was found during analysis
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';
@@ -661,10 +667,30 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
}
const uniqEdges = [];
+ const skippedDrugIds = new Set<string>();
+ const drugEdgeTypes = new Set<string>();
for (const edge of network.edges) {
const e = mapCustomEdge(edge, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
+ const isDrugEdge = e.to[0] === 'd' && e.to[1] === 'r';
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;
+ if (isDrugEdge) {
+ skippedDrugIds.add(e.to);
+ if (edge.actions) {
+ edge.actions.forEach(a => drugEdgeTypes.add(a));
+ }
+ if (edge.actions && this.networkHandler.activeNetwork.getSelectedDrugTargetType() && !edge.actions.includes(this.networkHandler.activeNetwork.getSelectedDrugTargetType())) {
+ continue;
+ }
+ const label = edge.actions && edge.actions.length > 0 ? edge.actions.join(',') : undefined;
+ skippedDrugIds.delete(e.to);
+ if (label) {
+ e.label = label;
+ }
+ }
+
+ this.networkHandler.activeNetwork.setDrugTargetTypes(Array.from(drugEdgeTypes));
+
const hash = e.from + '_' + e.to;
if (uniqEdges.indexOf(hash) === -1) {
uniqEdges.push(hash);
@@ -675,6 +701,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (!this.drugstoneConfig.currentConfig().selfReferences) {
edges = edges.filter(el => el.from !== el.to);
}
+ nodes = nodes.filter(n => !(n.drugstoneId && skippedDrugIds.has(n.drugstoneId)));
+ // if (this.networkHandler.activeNetwork.selectedDrugTargetType) {
+ // }
return {
nodes,
edges,
diff --git a/src/app/components/network/network-menu/network-menu.component.html b/src/app/components/network/network-menu/network-menu.component.html
index cf04a2a70b9f986f6e026d37e6353c7ec5adaa3a..1568447f2f0b71fdf56c2faad713136eb887708b 100644
--- a/src/app/components/network/network-menu/network-menu.component.html
+++ b/src/app/components/network/network-menu/network-menu.component.html
@@ -61,7 +61,7 @@
[ngClass]="{
'text-normal': drugstoneConfig.smallStyle
}"
- >Screenshot</span
+ >Screenshot</span
>
</button>
</div>
@@ -112,14 +112,14 @@
[ngClass]="{
'text-small': drugstoneConfig.smallStyle
}"
- >Tissue</span
+ >Tissue</span
>
<span
*ngIf="networkHandler.activeNetwork.selectedTissue"
[ngClass]="{
'text-small': drugstoneConfig.smallStyle
}"
- >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
+ >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
>
<app-fa-solid-icon
icon="angle-down"
@@ -182,7 +182,93 @@
networkHandler.activeNetwork.updateAdjacentDrugs($event, true)
"
></app-toggle-inplace>
+<!-- <div class="row is-full m-1" *ngIf="networkHandler.activeNetwork.showsAdjacentDrugs() || networkHandler.activeNetwork.hasDrugsLoaded()">-->
+<!-- <div-->
+<!-- class="dropdown network-footer-toolbar-element"-->
+<!-- [class.is-active]="networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- [ngClass]="{-->
+<!-- 'inner-dropdown': !networkHandler.networkSidebarOpen-->
+<!-- }"-->
+<!-- >-->
+<!-- <div class="dropdown-trigger">-->
+<!-- <button-->
+<!-- (click)="-->
+<!-- networkHandler.activeNetwork.drugTargetSelectionExpanded =-->
+<!-- !networkHandler.activeNetwork.drugTargetSelectionExpanded-->
+<!-- "-->
+<!-- class="button is-rounded"-->
+<!-- [disabled]="networkHandler.activeNetwork.getDrugTargetTypes().length === 0"-->
+<!-- [class.is-primary]="networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- aria-haspopup="true"-->
+<!-- aria-controls="dropdown-menu"-->
+<!-- pTooltip="Filter drug-target edges by drug action annotation."-->
+<!-- [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"-->
+<!-- tooltipPosition="left"-->
+<!-- [ngClass]="{-->
+<!-- 'is-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >-->
+<!-- <app-fa-solid-icon icon="crosshairs"></app-fa-solid-icon>-->
+
+<!-- <span-->
+<!-- *ngIf="!networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- [ngClass]="{-->
+<!-- 'text-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >Actions</span-->
+<!-- >-->
+<!-- <span-->
+<!-- *ngIf="networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- [ngClass]="{-->
+<!-- 'text-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >{{ networkHandler.activeNetwork.getSelectedDrugTargetType() }}</span-->
+<!-- >-->
+<!-- <app-fa-solid-icon-->
+<!-- icon="angle-down"-->
+<!-- classString="is-small last-item-in-button"-->
+<!-- *ngIf="networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- ></app-fa-solid-icon>-->
+<!-- <app-fa-solid-icon-->
+<!-- icon="angle-left"-->
+<!-- classString="is-small last-item-in-button"-->
+<!-- *ngIf="!networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- ></app-fa-solid-icon>-->
+<!-- </button>-->
+<!-- </div>-->
+<!-- <div class="dropdown-menu" id="drug-dropdown-menu" role="menu">-->
+<!-- <div class="dropdown-content tissue-dropdown">-->
+<!-- <div class="scroll-area">-->
+<!-- <a-->
+<!-- (click)="networkHandler.activeNetwork.updateAdjacentDrugSelection(null,true)"-->
+<!-- [class.is-active]="-->
+<!-- !networkHandler.activeNetwork.getSelectedDrugTargetType()-->
+<!-- "-->
+<!-- [ngClass]="{'text-small': drugstoneConfig.smallStyle}"-->
+<!-- class="dropdown-item"-->
+<!-- >-->
+<!-- None-->
+<!-- </a>-->
+<!-- <a-->
+<!-- *ngFor="-->
+<!-- let drugTargetType of networkHandler.activeNetwork.getDrugTargetTypes()-->
+<!-- "-->
+<!-- (click)="networkHandler.activeNetwork.updateAdjacentDrugSelection(drugTargetType, true)"-->
+<!-- [class.is-active]="-->
+<!-- networkHandler.activeNetwork.getSelectedDrugTargetType() && networkHandler.activeNetwork.getSelectedDrugTargetType() === drugTargetType-->
+<!-- "-->
+<!-- [ngClass]="{'text-small': drugstoneConfig.smallStyle}"-->
+<!-- class="dropdown-item"-->
+<!-- >-->
+<!-- {{ drugTargetType }}-->
+<!-- </a>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
</div>
+
<div
class="row is-full m-1"
*ngIf="
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 66c2bbe61aea7a12ba2335f489d00f48cc3a4975..3f2d8264fffd09aec2ce3e651860302f1894e2e6 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -23,6 +23,7 @@ import {NetworkHandlerService} from 'src/app/services/network-handler/network-ha
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 {Subject} from 'rxjs';
@Component({
selector: 'app-network',
@@ -60,6 +61,12 @@ export class NetworkComponent implements OnInit {
public adjacentDrugs = false;
+ public selectedDrugTargetType = new Subject<string | null>();
+ public selectedDrugTargetTypeLast: string | null = null;
+ public selectedDrugTargetType$ = this.selectedDrugTargetType.asObservable();
+ public drugTargetTypes: string[] = [];
+ public drugTargetTypesWithoutAdj: string[] = [];
+
public adjacentDisordersProtein = false;
public adjacentDisordersDrug = false;
public adjacentDrugList: Node[] = [];
@@ -77,8 +84,10 @@ export class NetworkComponent implements OnInit {
public currentViewEdges: NodeInteraction[];
public expressionExpanded = false;
+ public drugTargetSelectionExpanded = false;
public selectedTissue: Tissue | null = null;
+
// change this to true to have sidebar open per default
// public networkSidebarOpen = false;
@@ -130,6 +139,37 @@ export class NetworkComponent implements OnInit {
return {edges: this.inputNetwork.edges, nodes};
}
+ public getDrugTargetTypes() {
+ return this.drugTargetTypes;
+ }
+
+ public subscribeSelection(callback) {
+ this.selectedDrugTargetType$.subscribe(() => {
+ callback();
+ });
+ }
+
+ public setDrugTargetTypes(drugTargetTypes: string[], adj = false) {
+ if (adj) {
+ this.drugTargetTypesWithoutAdj = [...drugTargetTypes];
+ drugTargetTypes.filter(type => !this.drugTargetTypes.includes(type)).forEach((type) => {
+ this.drugTargetTypes.push(type);
+ });
+ } else {
+ this.drugTargetTypes = drugTargetTypes;
+ }
+ }
+
+ // TODO create method to get selected drug target type as string instead of subject or observable
+ public setSelectedDrugTargetType(value: string | null) {
+ this.selectedDrugTargetTypeLast = value;
+ this.selectedDrugTargetType.next(value);
+ }
+
+ public getSelectedDrugTargetType() {
+ return this.selectedDrugTargetTypeLast;
+ }
+
resetInputNetwork() {
const nodes = this.inputNetwork.nodes;
nodes.forEach(n => {
@@ -333,6 +373,38 @@ export class NetworkComponent implements OnInit {
});
}
+ public updateAdjacentDrugSelection(event, stabil: boolean) {
+ this.networkHandler.activeNetwork.drugTargetSelectionExpanded = false;
+ if (event === this.getSelectedDrugTargetType()) {
+ return;
+ }
+ this.setSelectedDrugTargetType(event);
+ if (this.networkHandler.activeNetwork.showsAdjacentDrugs()) {
+ this.updateAdjacentDrugs(false, false).then(() => {
+ // if (this.networkHandler.activeNetwork.hasDrugsLoaded()) {
+ // this.updateFoundDrugs(stabil).then(() => {
+ this.updateAdjacentDrugs(true, stabil);
+ // });
+ // } else {
+ // this.updateAdjacentDrugs(true, stabil);
+ // }
+ });
+ }
+ // else {
+ // this.updateFoundDrugs(stabil);
+ // }
+ }
+
+ public showsAdjacentDrugs(): boolean {
+ return this.adjacentDrugs;
+ }
+
+ public updateFoundDrugs(stabl: boolean): Promise<any> {
+ return new Promise<boolean>(async (resolve, reject) => {
+
+ });
+ }
+
public updateAdjacentDrugs(bool: boolean, stabl: boolean): Promise<any> {
return new Promise<boolean>(async (resolve, reject) => {
this.loadingScreen.stateUpdate(true);
@@ -345,12 +417,21 @@ export class NetworkComponent implements OnInit {
const proteinMap = this.getProteinMap();
this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licensedDatasets, this.nodeData.nodes.get()).then(response => {
const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
+ const availableDrugTargetTypes = new Set<string>();
for (const interaction of response.pdis) {
+ if (interaction.actions) {
+ for (const action of interaction.actions) {
+ availableDrugTargetTypes.add(action);
+ }
+ }
+ if (this.networkHandler.activeNetwork.getSelectedDrugTargetType() && interaction.actions && !interaction.actions.includes(this.networkHandler.activeNetwork.getSelectedDrugTargetType())) {
+ continue;
+ }
+ const label = interaction.actions && interaction.actions.length > 0 ? interaction.actions.join(',') : undefined;
const edge = mapCustomEdge({
from: interaction.protein,
to: interaction.drug
}, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
-
if (proteinMap[edge.from]) {
proteinMap[edge.from].forEach(from => {
if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
@@ -359,6 +440,9 @@ export class NetworkComponent implements OnInit {
const e = JSON.parse(JSON.stringify(edge));
e.from = from;
e.to = edge.to;
+ if (label) {
+ e.label = label;
+ }
this.adjacentDrugEdgesList.push(e);
if (!addedEdge[from]) {
addedEdge[from] = [edge.to];
@@ -367,11 +451,16 @@ export class NetworkComponent implements OnInit {
}
});
}
+ this.networkHandler.activeNetwork.setDrugTargetTypes(Array.from(availableDrugTargetTypes), true);
}
+ const addedDrugs = new Set<string>();
+ Object.values(addedEdge).forEach(targets => { // @ts-ignore
+ targets.forEach(t => addedDrugs.add(t));
+ });
for (const drug of response.drugs) {
drug.group = 'foundDrug';
drug.id = getDrugNodeId(drug);
- if (!existingDrugIDs.includes(drug.drugstoneId)) {
+ if (!existingDrugIDs.includes(drug.drugstoneId) && addedDrugs.has(drug.drugstoneId)) {
existingDrugIDs.push(drug.drugstoneId);
this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
}
@@ -633,7 +722,7 @@ export class NetworkComponent implements OnInit {
public hasDrugsLoaded(): boolean {
if (this.nodeData && this.nodeData.nodes) {
for (const node of this.nodeData.nodes.get()) {
- if (node.drugstoneType && node.drugstoneId === 'drug') {
+ if (node.drugstoneType && node.drugstoneType === 'drug') {
return true;
}
}
diff --git a/src/index.html b/src/index.html
index c25ff9799af8d2b4f27f96f27f8a8dc57b35ef78..29e12e9ebccb0a3ac048fbb4acab489dd983e7d6 100644
--- a/src/index.html
+++ b/src/index.html
@@ -115,8 +115,8 @@ 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"}}}'
- 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": "AGT", "to": "ACE", "group": "default"}, {"from": "AGT", "to": "GSDMB", "group": "default"}, {"from": "AGT", "to": "NDUFA3", "group": "default"}, {"from": "AGT", "to": "REN", "group": "default"}, {"from": "IL6", "to": "IL6R", "group": "default"}, {"from": "A2M", "to": "IL1B", "group": "default"}, {"from": "A2M", "to": "CPB2", "group": "default"}, {"from": "NLRP3", "to": "URB1", "group": "default"}, {"from": "NLRP3", "to": "HIST1H1B", "group": "default"}, {"from": "TLR4", "to": "TNFSF9", "group": "default"}, {"from": "TNFSF9", "to": "KLRG2", "group": "default"}, {"from": "RPL18", "to": "FCF1", "group": "default"}, {"from": "RPL18", "to": "URB1", "group": "default"}, {"from": "F5", "to": "F2", "group": "default"}, {"from": "F5", "to": "CCDC8", "group": "default"}, {"from": "F5", "to": "KLRG2", "group": "default"}, {"from": "IVL", "to": "FCF1", "group": "default"}, {"from": "IVL", "to": "KRT1", "group": "default"}, {"from": "IL6R", "to": "FANCB", "group": "default"}, {"from": "IL6R", "to": "CRYZL1", "group": "default"}, {"from": "IL6R", "to": "C17orf70", "group": "default"}, {"from": "IL6R", "to": "TBCK", "group": "default"}, {"from": "CPB2", "to": "F2", "group": "default"}, {"from": "CPB2", "to": "TINAG", "group": "default"}, {"from": "CCDC8", "to": "HEATR1", "group": "default"}, {"from": "CCDC8", "to": "PSMD1", "group": "default"}, {"from": "CCDC8", "to": "DARS", "group": "default"}, {"from": "SERPINB6", "to": "F2", "group": "default"}, {"from": "SERPINB6", "to": "SERPINB8", "group": "default"}, {"from": "SERPINB6", "to": "TMPRSS11A", "group": "default"}, {"from": "SERPINB6", "to": "C16orf70", "group": "default"}, {"from": "MBL2", "to": "KRT1", "group": "default"}, {"from": "IL24", "to": "NOTCH2", "group": "default"}, {"from": "IL24", "to": "CCR5", "group": "default"}, {"from": "F2", "to": "PLAT", "group": "default"}, {"from": "CCR5", "to": "PSMA5", "group": "default"}, {"from": "CCR5", "to": "AFP", "group": "default"}, {"from": "SERPINB8", "to": "FCF1", "group": "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"}]}'>
+ config='{"customEdges":{"default":true, "selectable":false},"licensedDatasets": true, "showAdvAnalysisContent":["drug-search", "enrichment-gprofiler", "enrichment-digest", "search-ndex"],"identifier":"symbol","showSimpleAnalysis":true, "title":"ROBUST output network", "taskDrugName": "Drug Search", "showLegendNodes": true, "showLegendEdges": true, "showSidebar": "left", "showOverview": true, "legendPos": "left", "legendClass": "legend", "showQuery": true, "showItemSelector": true,"showSimpleAnalysis": true,"showAdvAnalysis": true,"showSelection": true,"showTasks": true,"showNetworkMenu": "right","showLegend": true,"showNetworkMenuButtonExpression": true, "showNetworkMenuButtonScreenshot": true,"showNetworkMenuButtonExportGraphml": true,"showNetworkMenuButtonAdjacentDrugs": true,"showNetworkMenuButtonCenter": true,"showConnectGenes": true,"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": "KDR", "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": "AGT", "to": "ACE", "group": "default"}, {"from": "AGT", "to": "GSDMB", "group": "default"}, {"from": "AGT", "to": "NDUFA3", "group": "default"}, {"from": "AGT", "to": "REN", "group": "default"}, {"from": "IL6", "to": "IL6R", "group": "default"}, {"from": "A2M", "to": "IL1B", "group": "default"}, {"from": "A2M", "to": "CPB2", "group": "default"}, {"from": "NLRP3", "to": "URB1", "group": "default"}, {"from": "NLRP3", "to": "HIST1H1B", "group": "default"}, {"from": "TLR4", "to": "TNFSF9", "group": "default"}, {"from": "TNFSF9", "to": "KLRG2", "group": "default"}, {"from": "RPL18", "to": "FCF1", "group": "default"}, {"from": "RPL18", "to": "URB1", "group": "default"}, {"from": "F5", "to": "F2", "group": "default"}, {"from": "F5", "to": "CCDC8", "group": "default"}, {"from": "F5", "to": "KLRG2", "group": "default"}, {"from": "IVL", "to": "FCF1", "group": "default"}, {"from": "IVL", "to": "KRT1", "group": "default"}, {"from": "IL6R", "to": "FANCB", "group": "default"}, {"from": "IL6R", "to": "CRYZL1", "group": "default"}, {"from": "IL6R", "to": "C17orf70", "group": "default"}, {"from": "IL6R", "to": "TBCK", "group": "default"}, {"from": "CPB2", "to": "F2", "group": "default"}, {"from": "CPB2", "to": "TINAG", "group": "default"}, {"from": "CCDC8", "to": "HEATR1", "group": "default"}, {"from": "CCDC8", "to": "PSMD1", "group": "default"}, {"from": "CCDC8", "to": "DARS", "group": "default"}, {"from": "SERPINB6", "to": "F2", "group": "default"}, {"from": "SERPINB6", "to": "SERPINB8", "group": "default"}, {"from": "SERPINB6", "to": "TMPRSS11A", "group": "default"}, {"from": "SERPINB6", "to": "C16orf70", "group": "default"}, {"from": "MBL2", "to": "KRT1", "group": "default"}, {"from": "IL24", "to": "NOTCH2", "group": "default"}, {"from": "IL24", "to": "CCR5", "group": "default"}, {"from": "F2", "to": "PLAT", "group": "default"}, {"from": "CCR5", "to": "PSMA5", "group": "default"}, {"from": "CCR5", "to": "AFP", "group": "default"}, {"from": "SERPINB8", "to": "FCF1", "group": "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>