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AndiMajore authoredAndiMajore authored
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explorer-page.component.ts 24.48 KiB
import {
AfterViewInit,
Component,
ElementRef,
EventEmitter,
HostListener,
Input,
OnInit,
Output,
ViewChild,
} from '@angular/core';
import {
getDrugNodeId,
getWrapperFromNode,
legendContext,
Node,
NodeAttributeMap,
NodeInteraction,
Tissue,
Wrapper
} from '../../interfaces';
import {mapCustomEdge, mapCustomNode, mapNetexEdge, ProteinNetwork} from '../../main-network';
import {AnalysisService} from '../../services/analysis/analysis.service';
import {OmnipathControllerService} from '../../services/omnipath-controller/omnipath-controller.service';
import domtoimage from 'dom-to-image';
import {NetworkSettings} from '../../network-settings';
import {defaultConfig, EdgeGroup, IConfig, InteractionDatabase, NodeGroup} from '../../config';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
import {downLoadFile, removeDuplicateObjectsFromList} from '../../utils'
import * as merge from 'lodash/fp/merge';
import {AnalysisPanelComponent} from 'src/app/components/analysis-panel/analysis-panel.component';
declare var vis: 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": []}';
private networkPositions = undefined;
// set default config on init
public myConfig: IConfig = JSON.parse(JSON.stringify(defaultConfig));
@Input()
public onload: undefined | string;
@Input()
public id: undefined | string;
@Input()
public set config(config: string | undefined) {
if (typeof config === 'undefined') {
return;
}
if (this.id == null)
setTimeout(() => {
this.config = config;
}, 200);
// add settings to config
const configObj = JSON.parse(config);
this.myConfig = merge(this.myConfig, configObj);
// update Drugst.One according to the settings
// check if config updates affect network
let updateNetworkFlag = false; for (const key of Object.keys(configObj)) {
if (key === 'nodeGroups') {
this.setConfigNodeGroup(key, configObj[key]);
updateNetworkFlag = true;
} else if (key === 'edgeGroups') {
this.setConfigEdgeGroup(key, configObj[key]);
updateNetworkFlag = true;
} else if (key === 'interactions') {
this.getInteractions(configObj[key]);
} 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');
}
}
}
// 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
if (this.networkInternal !== undefined) {
// a network exists, save node positions
this.networkPositions = this.networkInternal.getPositions();
}
this.createNetwork();
}
}
@Input()
public set network(network: string | undefined) {
if (typeof network === 'undefined') {
return;
}
this.networkJSON = network;
this.createNetwork();
}
@Output()
public taskEvent = new EventEmitter<object>();
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: Node[];
public edges: NodeInteraction[];
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 adjacentDrugs = false;
public adjacentDrugList: Node[] = [];
public adjacentDrugEdgesList: Node[] = [];
public queryItems: Wrapper[] = [];
public showAnalysisDialog = false;
public showThresholdDialog = false;
public analysisDialogTarget: 'drug' | 'drug-target';
public showCustomProteinsDialog = false;
public selectedAnalysisToken: string | null = null;
@Input() set taskId(token: string | null) {
if (token == null || token.length === 0)
this.selectedAnalysisToken = null
this.selectedAnalysisToken = token;
}
public currentDataset = [];
public currentViewProteins: Node[];
public currentViewSelectedTissue: Tissue | null = null;
public currentViewNodes: Node[];
public currentViewEdges: NodeInteraction[];
public expressionExpanded = false;
public selectedTissue: Tissue | null = null;
public legendContext: legendContext = 'explorer';
// keys are node netexIds
public expressionMap: NodeAttributeMap = undefined;
@ViewChild('network', {static: false}) networkEl: ElementRef;
@ViewChild('networkWithLegend', {static: false}) networkWithLegendEl: ElementRef;
@ViewChild(AnalysisPanelComponent, {static: false})
private analysisPanel: AnalysisPanelComponent;
constructor(
public omnipath: OmnipathControllerService,
public analysis: AnalysisService,
public netex: NetexControllerService) {
this.showDetails = false;
this.analysis.subscribeList(async (items, selected) => {
// while (this.networkEl == null) {
// await setTimeout(() => {
// }, 200);
// }
// if (this.networkEl.nativeElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.id !== this.id)
// return;
// console.log("subcribe event on " + this.id)
// return if analysis panel is open or no nodes are loaded
if (this.selectedAnalysisToken || !this.nodeData.nodes) {
return; }
if (selected !== null) {
if (items == null || items.length === 0) {
return;
}
const updatedNodes = [];
for (const wrapper of items) {
// const node: Node = this.nodeData.nodes.get(wrapper.id);
const node = wrapper.data as Node;
if (!node) {
continue;
}
const pos = this.networkInternal.getPositions([wrapper.id]);
node.x = pos[wrapper.id].x;
node.y = pos[wrapper.id].y;
const nodeStyled = NetworkSettings.getNodeStyle(
node,
this.myConfig,
false,
selected,
1.0
)
nodeStyled.x = pos[wrapper.id].x;
nodeStyled.y = pos[wrapper.id].y;
updatedNodes.push(nodeStyled);
}
this.nodeData.nodes.update(updatedNodes);
} else {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
// const nodeSelected = this.analysis.idInSelection(node.id);
// if (node.group == 'default') {
// Object.assign(node, this.myConfig.nodeGroups.default);
// } else {
// Object.assign(node, this.myConfig.nodeGroups[node.group]);
// };
Object.assign(node, this.myConfig.nodeGroups[node.group]);
});
this.nodeData.nodes.update(updatedNodes);
}
});
}
@HostListener('window:resize', ['$event'])
onResize(event) {
this.setWindowWidth(document.getElementById('appWindow').getBoundingClientRect().width);
}
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(key: InteractionDatabase) {
let edges = [];
if (key == 'omnipath') {
const names = this.nodeData.nodes.map((node) => node.label);
const nameToNetworkId = {};
this.nodeData.nodes.map((node) => nameToNetworkId[node.label] = node.id);
edges = await this.omnipath.getInteractions(names, this.myConfig.identifier, nameToNetworkId); }
this.nodeData.edges.update(edges);
}
private async getNetwork() {
const network = JSON.parse(this.networkJSON);
if (this.myConfig.identifier === 'ensg') {
// @ts-ignore
network.nodes.forEach(node => {
node.id = this.removeEnsemblVersion(node.id);
});
// @ts-ignore
network.edges.forEach(edge => {
edge.from = this.removeEnsemblVersion(edge.from);
edge.to = this.removeEnsemblVersion(edge.to);
});
}
// map data to nodes in backend
if (network.nodes != null && network.nodes.length) {
network.nodes = await this.netex.mapNodes(network.nodes, this.myConfig.identifier);
}
if (this.myConfig.identifier === 'ensg') {
// remove possible duplicate IDs
network.nodes = removeDuplicateObjectsFromList(network.nodes, 'netexId');
}
// at this point, we have nodes synched with the backend
// use netexIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
network.nodes.forEach((node) => {
// set node label to original id before node id will be set to netex id
node.label = node.label ? node.label : node.id;
nodeIdMap[node.id] = node.netexId ? node.netexId : node.id;
node.id = nodeIdMap[node.id];
});
// adjust edge labels accordingly and filter
const edges = new Array();
network.edges.forEach(edge => {
edge.from = nodeIdMap[edge.from];
edge.to = nodeIdMap[edge.to];
// check if edges have endpoints
if (edge.from !== undefined && edge.to !== undefined) {
edges.push(edge);
}
});
// remove edges without endpoints
network.edges = edges;
this.proteins = network.nodes;
this.edges = network.edges;
}
private setWindowWidth(width: number) {
this.windowWidth = width;
this.smallStyle = this.windowWidth < 1250;
}
private zoomToNode(id: string) {
// get network object, depending on whether analysis is open or not
const network = this.selectedAnalysisToken ? this.analysisPanel.network : this.networkInternal;
this.nodeData.nodes.getIds(); const coords = network.getPositions(id)[id];
if (!coords) {
return;
}
let zoomScale = null;
if (id.startsWith('eff')) {
zoomScale = 1.0;
} else {
zoomScale = 3.0;
}
network.moveTo({
position: {x: coords.x, y: coords.y},
scale: zoomScale,
animation: true,
});
}
public graphmlLink() {
const data = {nodes: this.nodeData.nodes.get(), edges: this.nodeData.edges.get()}
this.netex.graphmlLink(data).subscribe(response => {
return downLoadFile(response, "application/xml");
})
}
public async openSummary(item: Wrapper, zoom: boolean) {
this.selectedWrapper = item;
if (zoom) {
this.zoomToNode(item.id);
}
this.showDetails = true;
}
public async closeSummary() {
this.selectedWrapper = null;
this.showDetails = false;
}
removeEnsemblVersion(versionId: string): string {
return versionId.startsWith('ENSG') ? versionId.split('.')[0] : versionId;
}
public async createNetwork() {
// if (this.networkEl == null) {
// setTimeout(() => {
// this.createNetwork();
// }, 200);
// return;
// }
// if (this.networkEl.nativeElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.id !== this.id)
// return;
console.log("network "+this.id+" is set up!")
this.analysis.resetSelection();
this.selectedWrapper = null;
// getNetwork synchronizes the input network with the database
await this.getNetwork();
this.proteinData = new ProteinNetwork(this.proteins, this.edges);
if (this.networkPositions) {
this.proteinData.updateNodePositions(this.networkPositions)
}
// TODO do we still need this?
// this.proteinData.linkNodes();
const {nodes, edges} = this.proteinData.mapDataToNetworkInput(this.myConfig);
if (this.myConfig.autofillEdges && nodes.length) {
const netexEdges = await this.netex.fetchEdges(nodes, this.myConfig.interactionProteinProtein);
edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, 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) => {
console.log("selected on node in "+this.id)
const nodeIds: Array<string> = properties.nodes;
if (nodeIds != null && nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
if (node.netexId === undefined || !node.netexId.startsWith('p')) {
// skip if node is not a protein mapped to backend
return;
}
const wrapper = getWrapperFromNode(node);
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 != null && 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.id);
}
this.currentViewNodes = this.nodeData.nodes;
this.currentViewEdges = this.nodeData.edges;
this.queryItems = [];
this.fillQueryItems(this.currentViewNodes);
if (this.selectedWrapper) {
this.networkInternal.selectNodes([this.selectedWrapper.id]);
}
}
fillQueryItems(hostProteins: Node[]) {
this.queryItems = [];
hostProteins.forEach((protein) => {
this.queryItems.push(getWrapperFromNode(protein));
});
this.currentViewProteins = this.proteins;
}
public queryAction(item: any) {
if (item) {
this.openSummary(item, true);
} }
public updatePhysicsEnabled(bool: boolean) {
this.physicsEnabled = bool;
this.networkInternal.setOptions({
physics: {
enabled: this.physicsEnabled,
stabilization: {
enabled: false,
},
}
});
}
public updateAdjacentDrugs(bool: boolean) {
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
for (const interaction of response.pdis) {
const edge = {from: interaction.protein, to: interaction.drug};
this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
}
for (const drug of response.drugs) {
drug.group = 'foundDrug';
drug.id = getDrugNodeId(drug)
this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
}
this.nodeData.nodes.add(this.adjacentDrugList);
this.nodeData.edges.add(this.adjacentDrugEdgesList);
})
this.legendContext = 'adjacentDrugs'
} else {
this.nodeData.nodes.remove(this.adjacentDrugList);
this.nodeData.edges.remove(this.adjacentDrugEdgesList);
this.adjacentDrugList = [];
this.adjacentDrugEdgesList = [];
this.legendContext = 'explorer'
}
}
/**
* 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 }) {
// make sure that return-groups (seeds, drugs, found nodes) are set
const defaultNodeGroups = JSON.parse(JSON.stringify(defaultConfig.nodeGroups));
// user merge function to do deep merge
nodeGroups = merge(defaultNodeGroups, nodeGroups);
// make sure all keys are set
Object.entries(nodeGroups).forEach(([key, group]) => {
if (!group.color && key !== 'selectedNode') {
console.error(`Group ${key} has no attribute 'color'.`);
}
if (!group.shape && key !== 'selectedNode') {
console.error(`Group ${key} has no attribute 'shape'.`);
}
if (!group.groupName && key !== 'selectedNode') {
console.error(`Group ${key} has no attribute 'groupName'.`);
}
// set default values in case they are not set by user
// these values are not mandatory but are neede to override default vis js styles after e.g. deselecting
// because vis js "remembers" styles even though they are removed
if (!group.borderWidth) {
group.borderWidth = 0;
} if (!group.borderWidthSelected) {
group.borderWidthSelected = 0;
}
if (!group.font) {
group.font = defaultConfig.nodeGroups.default.font;
}
// if color is set as string, add detail settings
if (typeof group.color === 'string') {
group.color = {
border: group.color,
background: group.color,
highlight: {
border: group.color,
background: group.color
}
}
}
// if image is given, set node shape to image
if (group.image) {
group.shape = 'image';
}
// implement nodeShadow option, it needs to be set for all nodes or none
group.shadow = this.myConfig.nodeShadow;
});
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 }) {
// make sure that default-groups are set
const defaultNodeGroups = JSON.parse(JSON.stringify(defaultConfig.edgeGroups));
edgeGroups = merge(defaultNodeGroups, edgeGroups);
// // 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;
}
// implement edgeShadow option, it needs to be set for all nodes or none
value.shadow = this.myConfig.edgeShadow;
});
this.myConfig[key] = edgeGroups;
}
public toImage() {
this.downloadDom(this.networkWithLegendEl.nativeElement).catch(error => {
console.error('Falling back to network only screenshot. Some components seem to be inaccessable, most likely the legend is a custom image with CORS access problems on the host server side.');
this.downloadDom(this.networkEl.nativeElement).catch(e => {
console.error('Some network content seems to be inaccessable for saving as a screenshot. This can happen due to custom images used as nodes. Please ensure correct CORS accessability on the images host server.');
console.error(e);
});
});
}
public downloadDom(dom: object) {
return domtoimage.toPng(dom, {bgcolor: '#ffffff'}).then((generatedImage) => {
const a = document.createElement('a');
a.href = generatedImage;
a.download = `Network.png`; a.click();
});
}
analysisWindowChanged($event: [any[], [Node[], Tissue], NodeInteraction[]]) {
if ($event) {
this.currentViewNodes = $event[0];
this.currentViewEdges = $event[2];
this.currentViewProteins = $event[1][0];
this.currentViewSelectedTissue = $event[1][1];
} else {
this.currentViewNodes = this.nodeData.nodes;
this.currentViewEdges = this.nodeData.edges;
this.currentViewProteins = this.proteins;
this.currentViewSelectedTissue = this.selectedTissue;
}
// changes for either way (analysis open and close)
this.selectedWrapper = null;
this.fillQueryItems(this.currentViewNodes);
}
gProfilerLink(): string {
// nodes in selection have netexId
const queryString = this.analysis.getSelection()
.filter(wrapper => wrapper.data.netexId.startsWith('p'))
.map(wrapper => wrapper.data.uniprotAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
'organism=hsapiens&' +
`query=${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) {
if (item.netexId === undefined) {
// nodes that are not mapped to backend remain untouched
continue;
}
const node: 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,
NetworkSettings.getNodeStyle(
node,
this.myConfig,
false,
this.analysis.inSelection(getWrapperFromNode(item)),
1.0
)
) updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
// delete expression values
this.expressionMap = undefined;
} else {
this.selectedTissue = tissue
const minExp = 0.3;
// filter out non-proteins, e.g. drugs
const proteinNodes = [];
this.nodeData.nodes.forEach(element => {
if (element.id.startsWith('p') && element.netexId !== undefined) {
proteinNodes.push(element);
}
});
this.netex.tissueExpressionGenes(this.selectedTissue, proteinNodes).subscribe((response) => {
this.expressionMap = response;
const updatedNodes = [];
// mapping from netex IDs to network IDs, TODO check if this step is necessary
const networkIdMappping = {}
this.nodeData.nodes.forEach(element => {
networkIdMappping[element.netexId] = element.id
});
const maxExpr = Math.max(...Object.values(this.expressionMap));
for (const [netexId, expressionlvl] of Object.entries(this.expressionMap)) {
const networkId = networkIdMappping[netexId]
const node = this.nodeData.nodes.get(networkId);
if (node === null) {
continue;
}
const wrapper = getWrapperFromNode(node)
const gradient = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
const pos = this.networkInternal.getPositions([networkId]);
node.x = pos[networkId].x;
node.y = pos[networkId].y;
Object.assign(node,
NetworkSettings.getNodeStyle(
node,
this.myConfig,
node.isSeed,
this.analysis.inSelection(wrapper),
gradient));
node.gradient = gradient;
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
})
}
this.currentViewSelectedTissue = this.selectedTissue;
}
emitTaskEvent(eventObject: object) {
this.taskEvent.emit(eventObject);
}
}