From 3e6d441c1383c40b382a1c4f261a912cf80d6446 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Thu, 23 Sep 2021 18:33:56 +0200
Subject: [PATCH] added drug-disorder connections
---
src/app/config.ts | 2 +-
.../explorer-page.component.html | 16 +++-
.../explorer-page/explorer-page.component.ts | 80 +++++++++++++++----
.../netex-controller.service.ts | 17 ++--
4 files changed, 88 insertions(+), 27 deletions(-)
diff --git a/src/app/config.ts b/src/app/config.ts
index b938f880..eeb8d482 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -165,7 +165,7 @@ export const defaultConfig: IConfig = {
background: '#ffa62f'
},
},
- shape: 'diamond',
+ shape: 'triangle',
type: 'default disorder type',
},
seedNode: {
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 0f1ba721..dc5e1158 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -301,13 +301,23 @@
></app-toggle>
<app-toggle
class="footer-buttons network-footer-toolbar-element"
- textOn="Disorders"
+ textOn="Disorders (protein)"
textOff="Off"
tooltipOn="Display adjacent disorders ON."
tooltipOff="Display adjacent disorders OFF."
[smallStyle]="smallStyle"
- [value]="adjacentDisorders"
- (valueChange)="updateAdjacentDisorders($event)"
+ [value]="adjacentDisordersProtein"
+ (valueChange)="updateAdjacentProteinDisorders($event)"
+ ></app-toggle>
+ <app-toggle
+ class="footer-buttons network-footer-toolbar-element"
+ textOn="Disorders (drugs)"
+ textOff="Off"
+ tooltipOn="Display adjacent disorders ON."
+ tooltipOff="Display adjacent disorders OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDisordersDrug"
+ (valueChange)="updateAdjacentDrugDisorders($event)"
></app-toggle>
<app-toggle
class="footer-buttons network-footer-toolbar-element"
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 2a156407..6662d944 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -152,12 +152,16 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private dumpPositions = false;
public physicsEnabled = false;
public adjacentDrugs = false;
- public adjacentDisorders = false;
+ public adjacentDisordersProtein = false;
+ public adjacentDisordersDrug = false;
public adjacentDrugList: Node[] = [];
public adjacentDrugEdgesList: Node[] = [];
- public adjacentDisorderList: Node[] = [];
- public adjacentDisorderEdgesList: Node[] = [];
+ public adjacentProteinDisorderList: Node[] = [];
+ public adjacentProteinDisorderEdgesList: Node[] = [];
+
+ public adjacentDrugDisorderList: Node[] = [];
+ public adjacentDrugDisorderEdgesList: Node[] = [];
public queryItems: Wrapper[] = [];
public showAnalysisDialog = false;
@@ -488,32 +492,76 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
}
- public updateAdjacentDisorders(bool: boolean){
- this.adjacentDisorders = bool;
- if (this.adjacentDisorders){
- this.netex.adjacentDisorders(this.nodeData.nodes).subscribe(response => {
- for (const interaction of response.pdis) {
+ public updateAdjacentProteinDisorders(bool: boolean){
+ this.adjacentDisordersProtein = bool;
+ if (this.adjacentDisordersProtein){
+ this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins').subscribe(response => {
+ for (const interaction of response.edges) {
const edge = {from: interaction.protein, to: interaction.disorder};
- this.adjacentDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ this.adjacentProteinDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ }
+ for (const disorder of response.disorders) {
+ disorder.group = 'defaultDisorder';
+ disorder.id = disorder.netexId;
+ this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
+ }
+ this.saveAddNodes(this.adjacentProteinDisorderList);
+ this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
+ });
+ this.legendContext = 'adjacentDisorders';
+ }else {
+ this.saveRemoveDisorders(this.adjacentProteinDisorderList);
+ this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
+ this.adjacentProteinDisorderList = [];
+ this.adjacentProteinDisorderEdgesList = [];
+ this.legendContext = 'explorer';
+ }
+ }
+
+ public updateAdjacentDrugDisorders(bool: boolean){
+ this.adjacentDisordersDrug = bool;
+ if (this.adjacentDisordersDrug){
+ this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs').subscribe(response => {
+ for (const interaction of response.edges) {
+ const edge = {from: interaction.drug, to: interaction.disorder};
+ this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
disorder.id = disorder.netexId;
- this.adjacentDisorderList.push(mapCustomNode(disorder, this.myConfig))
+ this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
}
- this.nodeData.nodes.add(this.adjacentDisorderList);
- this.nodeData.edges.add(this.adjacentDisorderEdgesList);
+ this.saveAddNodes(this.adjacentDrugDisorderList);
+ this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
});
this.legendContext = 'adjacentDisorders';
}else {
- this.nodeData.nodes.remove(this.adjacentDisorderList);
- this.nodeData.edges.remove(this.adjacentDisorderEdgesList);
- this.adjacentDisorderList = [];
- this.adjacentDisorderEdgesList = [];
+ this.saveRemoveDisorders(this.adjacentDrugDisorderList);
+ this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
+ this.adjacentDrugDisorderList = [];
+ this.adjacentDrugDisorderEdgesList = [];
this.legendContext = 'explorer';
}
}
+ public saveAddNodes(nodeList: Node[]){
+ const existing = this.nodeData.nodes.get().map(n=>n.id);
+ const toAdd = nodeList.filter(n=>existing.indexOf(n.id)===-1)
+ this.nodeData.nodes.add(toAdd);
+ }
+
+ public saveRemoveDisorders(nodeList: Node[]){
+ const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
+ if(other==null)
+ this.nodeData.nodes.remove(nodeList);
+ else{
+ const otherIds = other.map(d=>d.id);
+ const rest = nodeList.filter(d=>otherIds.indexOf(d.id)===-1)
+ this.nodeData.nodes.remove(rest)
+ }
+
+ }
+
public updateAdjacentDrugs(bool: boolean) {
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index 93546b84..0570859e 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -96,13 +96,16 @@ export class NetexControllerService {
return this.http.get(`${environment.backend}tissue_expression/`, {params});
}
- public adjacentDisorders(nodes: Node[]): Observable<any> {
- const genesBackendIds = nodes.map((node: Node) => node.netexId && !node.drugId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
- const drugsBackendIds = nodes.map((node: Node) => node.drugId && node.netexId && node.netexId.startsWith('dr') ? node.netexId.slice(1) : undefined).filter(id => id != null);
- const params = {
- proteins: genesBackendIds,
- drugs: drugsBackendIds,
- };
+ public adjacentDisorders(nodes: Node[], nodeType: string): Observable<any> {
+
+ const params = {};
+ if (nodeType === 'proteins') {
+ // @ts-ignore
+ params.proteins = nodes.map((node: Node) => node.netexId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
+ } else if (nodeType === 'drugs') {
+ // @ts-ignore
+ params.drugs = nodes.map((node: Node) => node.drugId && node.netexId.startsWith('dr') ? node.netexId.slice(2) : undefined).filter(id => id != null);
+ }
return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
}
--
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