diff --git a/src/app/api.service.ts b/src/app/api.service.ts
index 912e43e9354399a8b0df8dd41ba142b52c05359c..8e8ead34ef7538f8feda11eee02c9cbed1b33374 100644
--- a/src/app/api.service.ts
+++ b/src/app/api.service.ts
@@ -1,5 +1,5 @@
import { Injectable } from '@angular/core';
-import { HttpClient } from '@angular/common/http';
+import { HttpClient, HttpParams } from '@angular/common/http';
import { environment } from '../environments/environment';
@@ -11,8 +11,10 @@ export class ApiService {
constructor(private http: HttpClient) { }
- async getNetwork() {
- return this.http.get(networkUrl).toPromise();
+ async getNetwork(dataset: Array<[string, string]>) {
+ const data = JSON.stringify(dataset);
+ const params = new HttpParams().set('data', data);
+ return this.http.get(networkUrl, {params}).toPromise();
}
}
diff --git a/src/app/app.module.ts b/src/app/app.module.ts
index f1ec3c5593a7ec1c9c6289e8899c5e78f4af1df0..8d162a28b21be000b2a0f11cdc68970820024bb0 100644
--- a/src/app/app.module.ts
+++ b/src/app/app.module.ts
@@ -14,6 +14,7 @@ import {HttpClientModule} from '@angular/common/http';
import {QueryComponent} from './components/query/query.component';
import {BrowserAnimationsModule} from '@angular/platform-browser/animations';
import {ProteinAnalysisComponent} from './components/protein-analysis/protein-analysis.component';
+import { SelectDatasetComponent } from './components/select-dataset/select-dataset.component';
@NgModule({
@@ -24,6 +25,7 @@ import {ProteinAnalysisComponent} from './components/protein-analysis/protein-an
HomePageComponent,
QueryComponent,
ProteinAnalysisComponent,
+ SelectDatasetComponent,
],
imports: [
BrowserModule,
diff --git a/src/app/components/select-dataset/select-dataset.component.html b/src/app/components/select-dataset/select-dataset.component.html
new file mode 100644
index 0000000000000000000000000000000000000000..e6615bfdb7c6e20c57586cd6b8056759037a8222
--- /dev/null
+++ b/src/app/components/select-dataset/select-dataset.component.html
@@ -0,0 +1,9 @@
+<div class="content">
+ <ng-select [items]="datasetItems" bindLabel="label" bindValue="data" [virtualScroll]="true" class="custom"
+ placeholder="Select..." (change)="select($event)">
+ <ng-template ng-option-tmp let-item="item">
+ {{item.label}} <br/>
+ <small>{{item.datasets}}</small>
+ </ng-template>
+ </ng-select>
+</div>
diff --git a/src/app/components/select-dataset/select-dataset.component.scss b/src/app/components/select-dataset/select-dataset.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/app/components/select-dataset/select-dataset.component.spec.ts b/src/app/components/select-dataset/select-dataset.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b5e96d6e83f570baf5d5eebc56f7c3cea8c12e66
--- /dev/null
+++ b/src/app/components/select-dataset/select-dataset.component.spec.ts
@@ -0,0 +1,25 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { SelectDatasetComponent } from './select-dataset.component';
+
+describe('SelectDatasetComponent', () => {
+ let component: SelectDatasetComponent;
+ let fixture: ComponentFixture<SelectDatasetComponent>;
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ declarations: [ SelectDatasetComponent ]
+ })
+ .compileComponents();
+ }));
+
+ beforeEach(() => {
+ fixture = TestBed.createComponent(SelectDatasetComponent);
+ component = fixture.componentInstance;
+ fixture.detectChanges();
+ });
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+});
diff --git a/src/app/components/select-dataset/select-dataset.component.ts b/src/app/components/select-dataset/select-dataset.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..877eed0df4c905cf8967c4497a5af123924818da
--- /dev/null
+++ b/src/app/components/select-dataset/select-dataset.component.ts
@@ -0,0 +1,21 @@
+import {Component, EventEmitter, Input, Output} from '@angular/core';
+import {DataSet} from 'vis-data';
+import {Edge, Effect, Protein} from '../../pages/protein-network';
+
+@Component({
+ selector: 'app-select-dataset',
+ templateUrl: './select-dataset.component.html',
+ styleUrls: ['./select-dataset.component.scss']
+})
+
+export class SelectDatasetComponent {
+
+ @Output() selectDataset: EventEmitter<any> = new EventEmitter();
+
+ @Input() datasetItems: Array<{label: string, datasets: string, data: Array<[string, string]>}>;
+
+ public select(selectionItem) {
+ this.selectDataset.emit(selectionItem.data);
+ }
+
+}
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 30faf00d6839be5b306cf638cba752c51692eb84..aaaebed886c2e9d1eff538747c6a99a30b4202ae 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -4,6 +4,21 @@
<div class="content bar-left">
+ <div class="card bar">
+ <header class="card-header">
+ <p class="card-header-title">
+ <span class="icon">
+ <i class="fas fa-database" aria-hidden="true"></i>
+ </span> Choose Dataset
+ </p>
+ </header>
+ <div class="card-content">
+ <div class="content">
+ <app-select-dataset [datasetItems]="datasetItems" (selectDataset)="createNetwork($event)"></app-select-dataset>
+ </div>
+ </div>
+ </div>
+
<div class="card bar">
<header class="card-header">
<p class="card-header-title">
@@ -81,7 +96,8 @@
</div>
</div>
<footer class="card-footer">
- <button (click)="reset($event);" class="card-footer-item button is-danger">Reset
+ <button (click)="reset($event);" class="card-footer-item button is-danger">
+ Reset
</button>
</footer>
</div>
@@ -157,13 +173,13 @@
</div>
<div class="card bar">
- <!-- <header class="card-header">-->
- <!-- <p class="card-header-title">-->
- <!-- <span class="icon">-->
- <!-- <i class="fas fa-filter" aria-hidden="true"></i>-->
- <!-- </span> Summary-->
- <!-- </p>-->
- <!-- </header>-->
+ <header class="card-header">
+ <p class="card-header-title">
+ <span class="icon">
+ <i class="fas fa-filter" aria-hidden="true"></i>
+ </span> Summary
+ </p>
+ </header>
<div *ngIf="showDetails" class="card-content">
<div class="content">
<!-- <h2>Summary</h2>-->
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 6bb3cfb90c03386391e9398d55f3b6da1b0ede90..9be11bd6f93489343f4810875a8c33144c6bd610 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -1,6 +1,6 @@
import {AfterViewInit, Component, ElementRef, OnInit, ViewChild, Output, EventEmitter, HostListener} from '@angular/core';
import {ActivatedRoute, Router} from '@angular/router';
-import {Effect, Protein, ProteinNetwork} from '../protein-network';
+import {Edge, Effect, getDatasetFilename, Protein, ProteinNetwork} from '../protein-network';
import {HttpClient} from '@angular/common/http';
import {ApiService} from '../../api.service';
import {AnalysisService} from '../../analysis.service';
@@ -27,7 +27,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public proteinData: ProteinNetwork;
- public filteredProteins = [];
public proteins: any;
public effects: any;
public edges: any;
@@ -43,9 +42,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public queryItems = [];
public showAnalysisDialog = false;
-
-
-
+ public datasetItems: Array<{ label: string, datasets: string, data: Array<[string, string]> }> = [
+ {label: 'All', datasets: 'TUM & Krogan', data: [['TUM', 'HCoV'], ['TUM', 'SARS-CoV2'], ['Krogan', 'SARS-CoV2']]},
+ {label: 'HCoV', datasets: 'TUM', data: [['TUM', 'HCoV']]},
+ {label: 'CoV2', datasets: 'TUM & Krogan', data: [['TUM', 'SARS-CoV2'], ['Krogan', 'SARS-CoV2']]},
+ {label: 'CoV2', datasets: 'Krogan', data: [['Krogan', 'SARS-CoV2']]},
+ {label: 'CoV2', datasets: 'TUM', data: [['TUM', 'SARS-CoV2']]}];
@ViewChild('network', {static: false}) networkEl: ElementRef;
@@ -135,16 +137,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
async ngAfterViewInit() {
if (!this.network) {
- await this.createNetwork();
+ await this.createNetwork(this.datasetItems[0].data);
}
}
- fillQueryItems() {
- this.queryItems = this.filteredProteins;
- }
-
- private async getNetwork() {
- const data: any = await this.api.getNetwork();
+ private async getNetwork(dataset: Array<[string, string]>) {
+ const data: any = await this.api.getNetwork(dataset);
this.proteins = data.proteins;
this.effects = data.effects;
this.edges = data.edges;
@@ -158,6 +156,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private zoomToNode(id: string) {
const coords = this.network.getPositions(id)[id];
+ if (!coords) {
+ return;
+ }
this.network.moveTo({
position: {x: coords.x, y: coords.y},
scale: 1.0,
@@ -176,12 +177,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
await this.router.navigate(['explorer']);
}
-
- private async createNetwork() {
- await this.getNetwork();
+ public async createNetwork(dataset: Array<[string, string]>) {
+ await this.getNetwork(dataset);
this.proteinData = new ProteinNetwork(this.proteins, this.effects, this.edges);
if (!this.dumpPositions) {
- await this.proteinData.loadPositions(this.http);
+ await this.proteinData.loadPositions(this.http, dataset);
}
this.proteinData.linkNodes();
@@ -190,6 +190,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.proteinData.effects.sort((a, b) => {
return a.effectName.localeCompare(b.effectName);
});
+ this.viralProteinCheckboxes = [];
this.proteinData.effects.forEach((effect) => {
const effectName = effect.effectName;
if (effectNames.indexOf(effectName) === -1) {
@@ -251,6 +252,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.dumpPositions) {
this.network.on('stabilizationIterationsDone', () => {
+ // tslint:disable-next-line:no-console
+ console.log(`${getDatasetFilename(dataset)}`);
// tslint:disable-next-line:no-console
console.log(JSON.stringify(this.network.getPositions()));
});
@@ -261,12 +264,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.zoomToNode(`pg_${this.currentProteinAc}`);
}
- this.filteredProteins = this.proteins;
- this.fillQueryItems();
-
+ this.queryItems = this.proteins;
}
-
public async filterNodes() {
const visibleIds = new Set<string>(this.nodeData.nodes.getIds());
@@ -277,14 +277,14 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
const connectedProteinAcs = new Set<string>();
this.viralProteinCheckboxes.forEach((cb) => {
- const effects = [];
+ const effects: Array<Effect> = [];
this.proteinData.effects.forEach((effect) => {
if (effect.effectName === cb.data.effectName) {
effects.push(effect);
}
- });
+ });
effects.forEach((effect) => {
- const nodeId = `eff_${effect.effectId}`;
+ const nodeId = `eff_${effect.effectName}_${effect.virusName}_${effect.datasetName}`;
const found = visibleIds.has(nodeId);
if ((cb.checked || showAll) && !found) {
const node = this.mapEffectToNode(effect);
@@ -299,21 +299,22 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
connectedProteinAcs.add(pg.proteinAc);
});
}
- });
+ });
});
- this.filteredProteins = [];
+ const filteredProteins = [];
for (const protein of this.proteinData.proteins) {
const nodeId = `pg_${protein.proteinAc}`;
const contains = connectedProteinAcs.has(protein.proteinAc);
const found = visibleIds.has(nodeId);
if (contains) {
- this.filteredProteins.push(protein);
- }
- if (contains && !found) {
- const node = this.mapProteinToNode(protein);
- // this.nodeData.nodes.add(node);
- addNodes.set(node.id, node);
- } else if (!contains && found) {
+ filteredProteins.push(protein);
+
+ if (!found) {
+ const node = this.mapProteinToNode(protein);
+ // this.nodeData.nodes.add(node);
+ addNodes.set(node.id, node);
+ }
+ } else if (found) {
// this.nodeData.nodes.remove(nodeId);
removeIds.add(nodeId);
}
@@ -321,13 +322,18 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.nodeData.nodes.remove(Array.from(removeIds.values()));
this.nodeData.nodes.add(Array.from(addNodes.values()));
- this.fillQueryItems();
- }
+ this.queryItems = filteredProteins;
+ }
public updatePhysicsEnabled() {
this.network.setOptions({
- physics: {enabled: this.physicsEnabled},
+ physics: {
+ enabled: this.physicsEnabled,
+ stabilization: {
+ enabled: false,
+ },
+ }
});
}
@@ -341,22 +347,26 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
label: `${protein.proteinAc}`,
size: 10, font: '5px', color, shape: 'ellipse', shadow: false,
x: protein.x,
- y: protein.y
+ y: protein.y,
};
}
private mapEffectToNode(effect: Effect): any {
return {
- id: `eff_${effect.effectId}`,
- label: `${effect.effectId}`,
+ id: `eff_${effect.effectName}_${effect.virusName}_${effect.datasetName}`,
+ label: `${effect.effectName} (${effect.virusName}, ${effect.datasetName})`,
size: 10, color: '#118AB2', shape: 'box', shadow: true, font: {color: '#FFFFFF'},
x: effect.x,
- y: effect.y
+ y: effect.y,
};
}
- private mapEdge(edge: any): any {
- return {from: `pg_${edge.proteinAc}`, to: `eff_${edge.effectId}`, color: {color: '#afafaf', highlight: '#854141'}};
+ private mapEdge(edge: Edge): any {
+ return {
+ from: `pg_${edge.proteinAc}`,
+ to: `eff_${edge.effectName}_${edge.virusName}_${edge.datasetName}`,
+ color: {color: '#afafaf', highlight: '#854141'},
+ };
}
private mapDataToNodes(data: ProteinNetwork): { nodes: any[], edges: any[] } {
diff --git a/src/app/pages/protein-network.ts b/src/app/pages/protein-network.ts
index 8e5f97d3378e951a09e69fd277c53803f730ccd3..4a1614122236f3bb638dc28835f2d6a7324dcbdc 100644
--- a/src/app/pages/protein-network.ts
+++ b/src/app/pages/protein-network.ts
@@ -9,18 +9,23 @@ export interface Protein {
}
export interface Effect {
- effectId: string;
effectName: string;
- datasetName: string;
virusName: string;
+ datasetName: string;
proteins?: Protein[];
x?: number;
y?: number;
}
export interface Edge {
+ effectName: string;
+ virusName: string;
+ datasetName: string;
proteinAc: string;
- effectId: string;
+}
+
+export function getDatasetFilename(dataset: Array<[string, string]>): string {
+ return `network-${JSON.stringify(dataset).replace(/[\[\]\",]/g, '')}.json`;
}
export class ProteinNetwork {
@@ -28,8 +33,8 @@ export class ProteinNetwork {
constructor(public proteins: Protein[], public effects: Effect[], public edges: Edge[]) {
}
- public async loadPositions(http: HttpClient) {
- const nodePositions = await http.get(`assets/positions/network.json`).toPromise();
+ public async loadPositions(http: HttpClient, dataset: Array<[string, string]>) {
+ const nodePositions = await http.get(`assets/positions/${getDatasetFilename(dataset)}`).toPromise();
this.proteins.forEach((node) => {
const nodePosition = nodePositions[`pg_${node.proteinAc}`];
if (nodePosition) {
@@ -38,7 +43,7 @@ export class ProteinNetwork {
}
});
this.effects.forEach((node) => {
- const nodePosition = nodePositions[`eff_${node.effectId}`];
+ const nodePosition = nodePositions[`eff_${node.effectName}_${node.virusName}_${node.datasetName}`];
if (nodePosition) {
node.x = nodePosition.x;
node.y = nodePosition.y;
@@ -50,8 +55,8 @@ export class ProteinNetwork {
return this.proteins.find((p) => p.proteinAc === ac);
}
- public getEffect(name: string): Effect {
- return this.effects.find((eff) => eff.effectId === name);
+ public getEffect(name: string, virus: string, dataset: string): Effect {
+ return this.effects.find((eff) => eff.effectName === name && eff.virusName === virus && eff.datasetName === dataset);
}
public linkNodes() {
@@ -63,7 +68,7 @@ export class ProteinNetwork {
});
this.edges.forEach((edge) => {
const proteinGroup = this.getProtein(edge.proteinAc);
- const effect = this.getEffect(edge.effectId);
+ const effect = this.getEffect(edge.effectName, edge.virusName, edge.datasetName);
if (proteinGroup && effect) {
proteinGroup.effects.push(effect);
effect.proteins.push(proteinGroup);
diff --git a/src/assets/positions/network-KroganSARS-CoV2.json b/src/assets/positions/network-KroganSARS-CoV2.json
new file mode 100644
index 0000000000000000000000000000000000000000..751d0ee52f55e509e67bfbfe9773fdd5868c8a66
--- /dev/null
+++ b/src/assets/positions/network-KroganSARS-CoV2.json
@@ -0,0 +1 @@
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