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explorer-page.component.ts 16.96 KiB
import {
AfterViewInit,
Component, Directive,
ElementRef, HostListener, Input,
OnInit,
ViewChild
} from '@angular/core';
import {
NodeInteraction,
Node,
Wrapper,
getWrapperFromNode,
Tissue
} from '../../interfaces';
import {ProteinNetwork} from '../../main-network';
import {AnalysisService} from '../../services/analysis/analysis.service';
import {OmnipathControllerService} from '../../services/omnipath-controller/omnipath-controller.service';
import html2canvas from 'html2canvas';
import {NetworkSettings} from '../../network-settings';
import {defaultConfig, EdgeGroup, IConfig, NodeGroup} from '../../config';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
import { removeUnderscoreFromKeys } from 'src/app/utils';
// import * as 'vis' from 'vis-network';
// import {DataSet} from 'vis-data';
// import {vis} from 'src/app/scripts/vis-network.min.js';
declare var vis: any;
// import {Network, Data} from 'vis-network';
// declare var DataSet: any;
// declare var Network: any;
@Component({
selector: 'app-explorer-page',
templateUrl: './explorer-page.component.html',
styleUrls: ['./explorer-page.component.scss'],
})
export class ExplorerPageComponent implements OnInit, AfterViewInit {
private networkJSON = '{"nodes": [], "edges": []}';
// set default config on init
public myConfig: IConfig = JSON.parse(JSON.stringify(defaultConfig));
@Input()
public onload: undefined | string;
@Input()
public set config(config: string | undefined) {
if (typeof config === 'undefined') {
return;
}
// check if config updates affect network
let updateNetworkFlag = false;
const configObj = JSON.parse(config);
for (const key of Object.keys(configObj)) {
if (key === 'nodeGroups' ) {
this.setConfigNodeGroup(key, configObj[key]);
updateNetworkFlag = true;
// dont set the key here, will be set in function
continue;
} else if (key === 'edgeGroups') {
this.setConfigEdgeGroup(key, configObj[key])
updateNetworkFlag = true;
// dont set the key here, will be set in function
continue;
}
else if (key === 'interactions') {
this.getInteractions();
updateNetworkFlag = true; // dont set the key here, will be set in function
continue;
} else if (key === 'showLeftSidebar') {
if (configObj[key]) {
// shrink main column
document.getElementById('main-column').classList.remove('leftgone');
} else {
// extend main column
document.getElementById('main-column').classList.add('leftgone');
}
} else if (key === 'showRightSidebar') {
if (configObj[key]) {
// shrink main column
document.getElementById('main-column').classList.remove('rightgone');
} else {
// extend main column
document.getElementById('main-column').classList.add('rightgone');
}
}
this.myConfig[key] = configObj[key];
}
// trigger updates on config e.g. in legend
this.myConfig = {...this.myConfig};
if (updateNetworkFlag && typeof this.networkJSON !== 'undefined') {
// update network if network config has changed and networkJSON exists
this.createNetwork();
}
}
@Input()
public set network(network: string | undefined) {
if (typeof network === 'undefined') {
return;
}
this.networkJSON = network;
this.createNetwork();
}
public get network() {
return this.networkJSON;
}
public windowWidth = 0;
public smallStyle = false;
public showDetails = false;
public selectedWrapper: Wrapper | null = null;
public collapseAnalysisQuick = true;
public collapseAnalysis = true;
public collapseDetails = true;
public collapseTask = true;
public collapseSelection = true;
public collapseBaitFilter = true;
public collapseQuery = true;
public collapseData = true;
public collapseOverview = true;
public proteinData: ProteinNetwork;
public proteins: any;
public edges: any;
private networkInternal: any;
// this will store the vis Dataset
public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
private dumpPositions = false;
public physicsEnabled = false;
public queryItems: Wrapper[] = [];
public showAnalysisDialog = false;
public showThresholdDialog = false;
public analysisDialogTarget: 'drug' | 'drug-target';
public showCustomProteinsDialog = false;
public selectedAnalysisToken: string | null = null;
public currentDataset = [];
public currentViewProteins: Node[];
public currentViewSelectedTissue: Tissue | null = null;
public currentViewNodes: Node[];
public expressionExpanded = false;
public selectedTissue: Tissue | null = null;
@Input()
public textColor = 'red';
@ViewChild('network', {static: false}) networkEl: ElementRef;
constructor(
public omnipath: OmnipathControllerService,
public analysis: AnalysisService,
public netex: NetexControllerService) {
this.showDetails = false;
this.analysis.subscribeList((items, selected) => {
if (!this.nodeData.nodes) {
return;
}
if (selected !== null) {
if (items.length === 0) {
return;
}
const updatedNodes = [];
for (const item of items) {
const node = this.nodeData.nodes.get(item.id);
if (!node) {
continue;
}
const pos = this.networkInternal.getPositions([item.id]);
node.x = pos[item.id].x;
node.y = pos[item.id].y;
Object.assign(node, this.myConfig.nodeGroups[node.group]);
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
} else {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
const nodeSelected = this.analysis.idInSelection(node.id);
Object.assign(node, this.myConfig.nodeGroups[node.group]);
});
this.nodeData.nodes.update(updatedNodes);
}
});
}
@HostListener('window:resize', ['$event'])
onResize(event) {
this.setWindowWidth(event.target.innerWidth);
}
ngOnInit() {
this.setWindowWidth(document.getElementById('appWindow').getBoundingClientRect().width); }
async ngAfterViewInit() {
// TODO find out if this had a function? we were loading the network twice
// this.createNetwork();
if (this.onload) {
// tslint:disable-next-line:no-eval
eval(this.onload);
}
}
async getInteractions() {
const names = this.nodeData.nodes.map((node) => node.label);
const nameToNetworkId = {};
this.nodeData.nodes.map((node) => nameToNetworkId[node.label] = node.id);
const edges = await this.omnipath.getInteractions(names, this.myConfig.identifier, nameToNetworkId);
this.nodeData.edges.update(edges);
}
private async getNetwork() {
const network = JSON.parse(this.networkJSON);
// map data to nodes in backend
if (network.nodes.length) {
network.nodes = await this.netex.mapNodes(network.nodes, this.myConfig.identifier);
}
this.proteins = network.nodes;
this.edges = network.edges;
}
private setWindowWidth(width: number) {
this.windowWidth = width;
this.smallStyle = this.windowWidth < 1250;
}
private zoomToNode(id: string) {
this.nodeData.nodes.getIds();
const coords = this.networkInternal.getPositions(id)[id];
if (!coords) {
return;
}
let zoomScale = null;
if (id.startsWith('eff')) {
zoomScale = 1.0;
} else {
zoomScale = 3.0;
}
this.networkInternal.moveTo({
position: {x: coords.x, y: coords.y},
scale: zoomScale,
animation: true,
});
}
public async openSummary(item: Wrapper, zoom: boolean) {
this.selectedWrapper = item;
if (zoom) {
this.zoomToNode(item.nodeId);
}
this.showDetails = true;
}
public async closeSummary() {
this.selectedWrapper = null;
this.showDetails = false;
}
public async createNetwork() {
this.analysis.resetSelection();
this.selectedWrapper = null;
await this.getNetwork();
this.proteinData = new ProteinNetwork(this.proteins, this.edges);
this.proteinData.linkNodes();
const {nodes, edges} = this.proteinData.mapDataToNetworkInput(this.myConfig);
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
const container = this.networkEl.nativeElement;
const options = NetworkSettings.getOptions('main');
this.networkInternal = new vis.Network(container, this.nodeData, options);
this.networkInternal.on('doubleClick', (properties) => {
const nodeIds: Array<string> = properties.nodes;
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
const wrapper = getWrapperFromNode(node);
if (wrapper.data.netexId === undefined || !wrapper.data.netexId.startsWith('p')) {
// skip if node is not a protein mapped to backend
return
}
if (this.analysis.inSelection(node)) {
this.analysis.removeItems([wrapper]);
} else {
this.analysis.addItems([wrapper]);
}
}
});
this.networkInternal.on('click', (properties) => {
const nodeIds: Array<string> = properties.nodes;
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
const wrapper = getWrapperFromNode(node);
this.openSummary(wrapper, false);
} else {
this.closeSummary();
}
});
this.networkInternal.on('deselectNode', (properties) => {
this.closeSummary();
});
if (this.selectedWrapper) {
this.zoomToNode(this.selectedWrapper.nodeId);
}
this.queryItems = [];
this.fillQueryItems(this.proteins);
if (this.selectedWrapper) {
this.networkInternal.selectNodes([this.selectedWrapper.nodeId]);
}
}
fillQueryItems(hostProteins: Node[]) {
this.queryItems = [];
hostProteins.forEach((protein) => {
this.queryItems.push(getWrapperFromNode(protein));
});
this.currentViewNodes = this.nodeData.nodes;
this.currentViewProteins = this.proteins;
}
public queryAction(item: any) {
if (item) { this.openSummary(item, true);
}
}
public updatePhysicsEnabled(bool) {
this.physicsEnabled = bool;
this.networkInternal.setOptions({
physics: {
enabled: this.physicsEnabled,
stabilization: {
enabled: false,
},
}
});
}
/**
* Function to set the node group attribute in config
* Validates input NodeGroups and handles setting defaults
* @param key
* @param values
*/
public setConfigNodeGroup(key: string, nodeGroups: { [key: string]: NodeGroup}) {
if (nodeGroups === undefined || !Object.keys(nodeGroups).length) {
// if node groups are not set or empty, use default node group(s)
this.myConfig[key] = defaultConfig.nodeGroups;
// stop if nodeGroups do not contain any information
return
}
// // do not allow '_' in node Group names since it causes problems with backend
// nodeGroups = removeUnderscoreFromKeys(nodeGroups)
// make sure all keys are set
Object.entries(nodeGroups).forEach(([key, group]) => {
if (!('detailShowLabel' in group)) {
// use detailShowLabel default value if not set
group['detailShowLabel'] = defaultConfig.nodeGroups.default.detailShowLabel;
}
})
// make sure that return-groups (seeds, drugs, found nodes) are set
const defaultNodeGroups = JSON.parse(JSON.stringify(defaultConfig.nodeGroups));
// if user has set nodeGroups, do not use group "default"
delete defaultNodeGroups.default;
// if user has not set the return-groups, take the defaults
nodeGroups = {...defaultNodeGroups, ...nodeGroups}
// override default node groups
this.myConfig[key] = nodeGroups;
}
/**
* Function to set the edge group attribute in config
* Validates input EdgeGroups and handles setting defaults
* @param key
* @param values
*/
public setConfigEdgeGroup(key: string, edgeGroups: { [key: string]: EdgeGroup}) {
if (edgeGroups === undefined || !Object.keys(edgeGroups).length) {
// if edge groups are not set or empty, use default edge group(s)
this.myConfig[key] = defaultConfig.edgeGroups;
// stop if edgeGroups do not contain any information
return
}
// // do not allow '_' in node Group names since it causes problems with backend
// edgeGroups = removeUnderscoreFromKeys(edgeGroups)
// make sure all keys are set Object.entries(edgeGroups).forEach(([key, value]) => {
if (!('dashes' in value)) {
// use dashes default value if not set
value['dashes'] = defaultConfig.edgeGroups.default.dashes;
}
})
// override default node groups
this.myConfig[key] = edgeGroups;
}
public toCanvas() {
html2canvas(this.networkEl.nativeElement).then((canvas) => {
const generatedImage = canvas.toDataURL('image/png').replace('image/png', 'image/octet-stream');
const a = document.createElement('a');
a.href = generatedImage;
a.download = `Network.png`;
a.click();
});
}
analysisWindowChanged($event: [any[], [Node[], Tissue]]) {
if ($event) {
this.currentViewNodes = $event[0];
this.currentViewProteins = $event[1][0];
this.currentViewSelectedTissue = $event[1][1];
} else {
this.currentViewNodes = this.nodeData.nodes;
this.currentViewProteins = this.proteins;
this.currentViewSelectedTissue = this.selectedTissue;
}
}
gProfilerLink(): string {
// nodes in selection have netexId
const queryString = this.analysis.getSelection()
.filter(wrapper => wrapper.data.netexId.startsWith('p'))
.map(wrapper => wrapper.data.uniprotAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
'organism=hsapiens&' +
`query=${queryString}&` +
'ordered=false&' +
'all_results=false&' +
'no_iea=false&' +
'combined=false&' +
'measure_underrepresentation=false&' +
'domain_scope=annotated&' +
'significance_threshold_method=g_SCS&' +
'user_threshold=0.05&' +
'numeric_namespace=ENTREZGENE_ACC&' +
'sources=GO:MF,GO:CC,GO:BP,KEGG,TF,REAC,MIRNA,HPA,CORUM,HP,WP&' +
'background=';
}
public selectTissue(tissue: Tissue | null) {
this.expressionExpanded = false;
if (!tissue) {
this.selectedTissue = null;
const updatedNodes = [];
for (const item of this.proteins) {
const node = this.nodeData.nodes.get(item.nodeId);
if (!node) {
continue;
}
const pos = this.networkInternal.getPositions([item.nodeId]);
node.x = pos[item.nodeId].x;
node.y = pos[item.nodeId].y;
// Object.assign(node,
// NetworkSettings.getNodeStyle(
// node.wrapper.type, // node.isSeed,
// this.analysis.inSelection(item),
// undefined,
// undefined,
// 1.0));
node.wrapper = item;
node.gradient = 1.0;
// protein.expressionLevel = undefined;
(node.wrapper.data as Node).expressionLevel = undefined;
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
} else {
this.selectedTissue = tissue;
const minExp = 0.3;
// const params = new HttpParams().set('tissue', `${tissue.id}`).set('data', JSON.stringify(this.currentDataset));
// this.http.get<any>(
// `${environment.backend}tissue_expression/`, {params})
// .subscribe((levels) => {
// const updatedNodes = [];
// const maxExpr = Math.max(...levels.map(lvl => lvl.level));
// for (const lvl of levels) {
// const item = getWrapperFromNode(lvl.protein);
// const node = this.nodeData.nodes.get(item.nodeId);
// if (!node) {
// continue;
// }
// const gradient = lvl.level !== null ? (Math.pow(lvl.level / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
// const pos = this.network.getPositions([item.nodeId]);
// node.x = pos[item.nodeId].x;
// node.y = pos[item.nodeId].y;
// Object.assign(node,
// NetworkSettings.getNodeStyle(
// node.wrapper.type,
// node.isSeed,
// this.analysis.inSelection(item),
// undefined,
// undefined,
// gradient));
// node.wrapper = item;
// node.gradient = gradient;
// this.proteins.find(prot => getProteinNodeId(prot) === item.nodeId).expressionLevel = lvl.level;
// (node.wrapper.data as Protein).expressionLevel = lvl.level;
// updatedNodes.push(node);
// }
// this.nodeData.nodes.update(updatedNodes);
// });
}
this.currentViewSelectedTissue = this.selectedTissue;
}
}