From ab3a699dcf00df5f34d4750dd942b7cdb44e3eb2 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Wed, 22 Sep 2021 19:26:48 +0200
Subject: [PATCH] added add disorders by protein association to explorer
---
.../network-legend.component.ts | 14 ++++---
src/app/config.ts | 13 ++++++
src/app/interfaces.ts | 11 ++++-
.../explorer-page.component.html | 11 ++++-
.../explorer-page/explorer-page.component.ts | 31 +++++++++++++-
src/app/services/analysis/analysis.service.ts | 2 +-
.../netex-controller.service.ts | 42 ++++++++++++-------
7 files changed, 98 insertions(+), 26 deletions(-)
diff --git a/src/app/components/network-legend/network-legend.component.ts b/src/app/components/network-legend/network-legend.component.ts
index 431fbe69..79c83120 100644
--- a/src/app/components/network-legend/network-legend.component.ts
+++ b/src/app/components/network-legend/network-legend.component.ts
@@ -13,17 +13,19 @@ export class NetworkLegendComponent implements OnInit {
@Input() config: IConfig;
private contextNodeGroupsToDelete = {
- 'explorer': ['foundNode', 'foundDrug', 'seedNode', 'default'],
- 'adjacentDrugs': ['foundNode', 'seedNode', 'default'],
- 'drugTarget': ['foundDrug', 'seedNode', 'default'],
- 'drug': ['seedNode', 'default'],
- 'drugTargetAndSeeds': ['foundDrug', 'default'],
- 'drugAndSeeds': ['default']
+ 'explorer': ['foundNode', 'foundDrug', 'seedNode', 'default', 'defaultDisorder'],
+ 'adjacentDrugs': ['foundNode', 'seedNode', 'default', 'defaultDisorder'],
+ 'adjacentDisorders': ['foundDrug', 'foundNode', 'seedNode', 'default'],
+ 'drugTarget': ['foundDrug', 'seedNode', 'default', 'defaultDisorder'],
+ 'drug': ['seedNode', 'default', 'defaultDisorder'],
+ 'drugTargetAndSeeds': ['foundDrug', 'default', 'defaultDisorder'],
+ 'drugAndSeeds': ['default', 'defaultDisorder']
}
private contextEdgeGroupsToDelete = {
'explorer': ['default'],
'adjacentDrugs': ['default'],
+ 'adjacentDisorders': ['default'],
'drugTarget': ['default'],
'drug': ['default'],
'drugTargetAndSeeds': ['default'],
diff --git a/src/app/config.ts b/src/app/config.ts
index 54e4461f..b938f880 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -155,6 +155,19 @@ export const defaultConfig: IConfig = {
shape: 'diamond',
type: 'default drug type',
},
+ defaultDisorder: {
+ groupName: 'Disorders',
+ color: {
+ border: '#ffa62f',
+ background: '#ffa62f',
+ highlight: {
+ border: '#ffa62f',
+ background: '#ffa62f'
+ },
+ },
+ shape: 'diamond',
+ type: 'default disorder type',
+ },
seedNode: {
groupName: 'Seed Nodes',
shape: 'triangle',
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 2c467aad..3bebde46 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -6,6 +6,7 @@ export interface Node {
id: string;
type: string;
netexId?: string;
+ drugId?:string;
uniprotAc?: string;
ensg?: Array<string>;
group?: string;
@@ -31,8 +32,8 @@ export interface Tissue {
name: string;
}
-export type legendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
-'drugTargetAndSeeds' | 'drugAndSeeds';
+export type legendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
+'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders';
/// netexId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
@@ -120,6 +121,12 @@ export function getDrugNodeId(drug: Drug) {
return drug.netexId
}
+// export function getDisorderNodeId(disorder: Disorder) {
+// /**
+// * Returns backend_id of Drug object
+// */
+// return disorder.netexId
+
export function getNodeId(node: Node) {
/**
* Returns backend_id of Gene object
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 4b426b8e..0f1ba721 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -299,7 +299,16 @@
[value]="adjacentDrugs"
(valueChange)="updateAdjacentDrugs($event)"
></app-toggle>
-
+ <app-toggle
+ class="footer-buttons network-footer-toolbar-element"
+ textOn="Disorders"
+ textOff="Off"
+ tooltipOn="Display adjacent disorders ON."
+ tooltipOff="Display adjacent disorders OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDisorders"
+ (valueChange)="updateAdjacentDisorders($event)"
+ ></app-toggle>
<app-toggle
class="footer-buttons network-footer-toolbar-element"
textOn="Animation"
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 3f2e7700..2a156407 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -152,9 +152,13 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private dumpPositions = false;
public physicsEnabled = false;
public adjacentDrugs = false;
+ public adjacentDisorders = false;
public adjacentDrugList: Node[] = [];
public adjacentDrugEdgesList: Node[] = [];
+ public adjacentDisorderList: Node[] = [];
+ public adjacentDisorderEdgesList: Node[] = [];
+
public queryItems: Wrapper[] = [];
public showAnalysisDialog = false;
public showThresholdDialog = false;
@@ -427,7 +431,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
}
});
-
this.networkInternal.on('click', (properties) => {
const nodeIds: Array<string> = properties.nodes;
if (nodeIds != null && nodeIds.length > 0) {
@@ -485,6 +488,32 @@ 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) {
+ const edge = {from: interaction.protein, to: interaction.disorder};
+ this.adjacentDisorderEdgesList.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.nodeData.nodes.add(this.adjacentDisorderList);
+ this.nodeData.edges.add(this.adjacentDisorderEdgesList);
+ });
+ this.legendContext = 'adjacentDisorders';
+ }else {
+ this.nodeData.nodes.remove(this.adjacentDisorderList);
+ this.nodeData.edges.remove(this.adjacentDisorderEdgesList);
+ this.adjacentDisorderList = [];
+ this.adjacentDisorderEdgesList = [];
+ this.legendContext = 'explorer';
+ }
+ }
+
public updateAdjacentDrugs(bool: boolean) {
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index 5278217d..0752bd50 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -358,7 +358,7 @@ export class AnalysisService {
const watch = async () => {
if (this.tokens.length > 0) {
const newtasks = await this.getTasks();
- if (newtasks.length === 0)
+ if(newtasks.length === 0)
return;
const newTaskIds = newtasks.map(t => t.token.toString());
this.tasks = newtasks.concat(this.tasks.filter(t => newTaskIds.indexOf(t.token) === -1));
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index bfc7e285..145db2b7 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -1,17 +1,18 @@
-import { Injectable } from '@angular/core';
+import {Injectable} from '@angular/core';
import {environment} from '../../../environments/environment';
import {HttpClient, HttpParams} from '@angular/common/http';
import {AlgorithmType, QuickAlgorithmType} from '../analysis/analysis.service';
-import { Observable } from 'rxjs';
-import { Tissue, Node, EdgeType} from 'src/app/interfaces';
-import { InteractionDrugProteinDB, InteractionProteinProteinDB } from 'src/app/config';
+import {Observable} from 'rxjs';
+import {Tissue, Node, EdgeType} from 'src/app/interfaces';
+import {InteractionDrugProteinDB, InteractionProteinProteinDB} from 'src/app/config';
@Injectable({
providedIn: 'root'
})
export class NetexControllerService {
- constructor(private http: HttpClient) { }
+ constructor(private http: HttpClient) {
+ }
public async getTask(token): Promise<any> {
/**
@@ -42,9 +43,9 @@ export class NetexControllerService {
}
public async getTaskResultGene(token): Promise<any> {
- /**
- * returns promise of gene view of task result of COMPLETED task
- */
+ /**
+ * returns promise of gene view of task result of COMPLETED task
+ */
return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=genes`).toPromise();
}
@@ -55,7 +56,7 @@ export class NetexControllerService {
return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=cancer_driver_genes`).toPromise();
}
- public async postTask(algorithm: QuickAlgorithmType | AlgorithmType, target, parameters, ) {
+ public async postTask(algorithm: QuickAlgorithmType | AlgorithmType, target, parameters,) {
/**
* sends a task to task service
*/
@@ -87,28 +88,39 @@ export class NetexControllerService {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
- // slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map( (node: Node) => node.netexId ? node.netexId.slice(1) : undefined);
+ // slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
+ const genesBackendIds = nodes.map((node: Node) => node.netexId ? node.netexId.slice(1) : undefined);
const params = new HttpParams()
.set('tissue', tissue.netexId)
.set('proteins', JSON.stringify(genesBackendIds));
return this.http.get(`${environment.backend}tissue_expression/`, {params});
}
+ public adjacentDisorders(nodes: Node[]): Observable<any> {
+ const genesBackendIds = nodes.map((node: Node) => node.netexId && !node.drugId ? node.netexId.slice(1) : undefined).filter(id => id != null);
+ const drugsBackendIds = nodes.map((node: Node) => node.drugId && node.netexId ? node.netexId.slice(1) : undefined).filter(id => id != null);
+ const params = {
+ proteins: genesBackendIds,
+ drugs: drugsBackendIds,
+ };
+ console.log(params)
+ return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
+ }
+
public adjacentDrugs(pdiDataset: InteractionDrugProteinDB, nodes: Node[]): Observable<any> {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
- // slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map( (node: Node) => node.netexId ? node.netexId.slice(1) : undefined);
+ // slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
+ const genesBackendIds = nodes.map((node: Node) => node.netexId ? node.netexId.slice(1) : undefined).filter(id => id != null);
const params = {
pdi_dataset: pdiDataset,
proteins: genesBackendIds
- }
+ };
return this.http.post<any>(`${environment.backend}adjacent_drugs/`, params);
}
- public graphmlLink(graph_data: {edges: EdgeType[], nodes: Node[]}) {
+ public graphmlLink(graph_data: { edges: EdgeType[], nodes: Node[] }) {
/**
* Sends complete graph data to backend where it is written to graphml File.
* The file is returned as download for the user.
--
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