diff --git a/src/app/config.ts b/src/app/config.ts
index 4d792077d0b6660b8516993c7f061fe0bf25817a..31da31f923b7f9303dcd825526b1d85a6b04ab78 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -32,7 +32,7 @@ export type InteractionDrugProteinDB = 'NeDRex' | 'DrugBank' | 'DrugCentral' | '
export type InteractionProteinProteinDB = 'NeDRex' | 'BioGRID' | 'IID' | 'IntAct' | 'STRING' | 'APID';
export type IndicationDrugDisorderDB = 'NeDRex' | 'CTD' | 'DrugCentral' | 'DrugBank';
export type AssociatedProteinDisorderDB = 'NeDRex' | 'DisGeNET' | 'OMIM';
-export type AdvAnalysisContentTypes = 'drug-target-search' | 'drug-search' | 'enrichment-gprofiler';
+export type AdvAnalysisContentTypes = 'drug-target-search' | 'drug-search' | 'enrichment-gprofiler' | 'enrichment-digest';
// TODO: should this be external or integrated in the backend?
@@ -145,7 +145,7 @@ export const defaultConfig: IConfig = {
showItemSelector: true,
showSimpleAnalysis: true,
showAdvAnalysis: true,
- showAdvAnalysisContent: ['drug-search', 'drug-target-search', 'enrichment-gprofiler'],
+ showAdvAnalysisContent: ['drug-search', 'drug-target-search', 'enrichment-gprofiler', 'enrichment-digest'],
showSelection: true,
showTasks: true,
showNetworkMenu: 'right',
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 28f4e53a3f70ae5e56c55dd190ef40f23cb0a7f8..e76a67a66ee48bd285c8ce9ebad3bcc14eae6873 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -281,7 +281,7 @@
<div class="control">
<a
*ngIf="analysis.getCount() > 0"
- [href]="gProfilerLink()"
+ (click)="openExternal(gProfilerLink())"
target="_blank"
[ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
class="button is-primary is-fullwidth is-rounded has-tooltip"
@@ -298,7 +298,7 @@
<span
[ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
>
- Enrichment Analysis
+ g:Profiler Enrichment Analysis
</span>
</a>
<a
@@ -319,7 +319,54 @@
<span
[ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
>
- Enrichment Analysis
+ g:Profiler Enrichment Analysis
+ </span>
+ </a>
+ </div>
+ </div>
+ <div class="field" *ngIf="!drugstoneConfig.config.showAdvAnalysisContent || drugstoneConfig.config.showAdvAnalysisContent.includes('enrichment-digest')">
+ <div class="control">
+ <a
+ *ngIf="analysis.getCount() > 0"
+ (click)="openDigest()"
+ target="_blank"
+ [ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
+ class="button is-primary is-fullwidth is-rounded has-tooltip"
+ pTooltip="Use enrichment analysis via DIGEST (external)."
+ [tooltipStyleClass]="
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
+ tooltipPosition="top"
+ >
+ <app-fa-solid-icon
+ classString="first-item-in-button"
+ icon="external-link-alt"
+ ></app-fa-solid-icon>
+ <span
+ [ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
+ >
+ DIGEST Enrichment Analysis
+ </span>
+ </a>
+ <a
+ *ngIf="analysis.getCount() === 0"
+ disabled
+ [ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
+ class="button is-primary is-fullwidth is-rounded has-tooltip"
+ pTooltip="Use enrichment analysis via DIGEST (external)."
+ [tooltipStyleClass]="
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
+ tooltipPosition="top"
+ >
+ <app-fa-solid-icon
+ icon="external-link-alt"
+ classString="first-item-in-button"
+ ></app-fa-solid-icon>
+ <span
+ [ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
+ >
+ DIGEST Enrichment Analysis
</span>
</a>
</div>
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 2292ba0017fa364aec1794b31dc612f1d73f9990..b2ca36514a2e6d180894a12bac0581fd78786c0a 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -78,7 +78,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
try {
this.networkJSON = JSON.stringify(typeof network === 'string' ? JSON5.parse(network) : network);
} catch {
- console.log('ERROR: Failed parsing input network')
+ console.log('ERROR: Failed parsing input network');
}
this.activateConfig();
}
@@ -120,8 +120,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public selectedAnalysisToken: string | null = null;
@Input() set taskId(token: string | null) {
- if (token == null || token.length === 0)
- this.selectedAnalysisToken = null
+ if (token == null || token.length === 0) {
+ this.selectedAnalysisToken = null;
+ }
this.selectedAnalysisToken = token;
}
@@ -158,7 +159,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
selected,
this.networkHandler.activeNetwork.getGradient(wrapper.id),
this.networkHandler.activeNetwork.nodeRenderer
- )
+ );
nodeStyled.x = pos[wrapper.id].x;
nodeStyled.y = pos[wrapper.id].y;
updatedNodes.push(nodeStyled);
@@ -257,36 +258,41 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
let node_map = {};
nodes.filter(n => n.drugstoneType === 'protein').forEach(node => {
if (typeof node.drugstoneId === 'string') {
- if (node_map[node.drugstoneId])
+ if (node_map[node.drugstoneId]) {
node_map[node.drugstoneId].push(node.id);
- else
+ } else {
node_map[node.drugstoneId] = [node.id];
+ }
} else {
node.drugstoneId.forEach(n => {
- if (node_map[n])
+ if (node_map[n]) {
node_map[n].push(node.id);
- else
+ } else {
node_map[n] = [node.id];
- })
+ }
+ });
}
- })
+ });
const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein, this.drugstoneConfig.config.licensedDatasets);
edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.config, node_map)).flatMap(e => e));
}
- const edge_map = {}
+ const edge_map = {};
edges = edges.filter(edge => {
- if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1)
- return false
- if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !== -1)
- return false
- if (!edge_map[edge.from])
- edge_map[edge.from] = [edge.to]
- else
- edge_map[edge.from].push(edge.to)
- return true
- })
+ if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1) {
+ return false;
+ }
+ if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !== -1) {
+ return false;
+ }
+ if (!edge_map[edge.from]) {
+ edge_map[edge.from] = [edge.to];
+ } else {
+ edge_map[edge.from].push(edge.to);
+ }
+ return true;
+ });
// @ts-ignore
if (!this.drugstoneConfig.selfReferences) {
@@ -375,10 +381,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
if (network.edges != null)
// @ts-ignore
+ {
network.edges.forEach(edge => {
edge.from = this.removeEnsemblVersion(edge.from);
edge.to = this.removeEnsemblVersion(edge.to);
});
+ }
}
// map data to nodes in backend
@@ -401,12 +409,13 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
// adjust edge labels accordingly and filter
const edges = new Array();
- if (network.edges != null)
+ if (network.edges != null) {
network.edges.forEach(edge => {
if (edge.from !== undefined && edge.to !== undefined) {
edges.push(edge);
}
});
+ }
// remove edges without endpoints
network.edges = edges;
this.networkHandler.activeNetwork.inputNetwork = network;
@@ -423,7 +432,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.networkHandler.activeNetwork.selectedWrapper = item;
// add expression information if loaded
if (this.networkHandler.activeNetwork.expressionMap && this.networkHandler.activeNetwork.selectedWrapper.id in this.networkHandler.activeNetwork.expressionMap) {
- this.networkHandler.activeNetwork.selectedWrapper.expression = this.networkHandler.activeNetwork.expressionMap[this.networkHandler.activeNetwork.selectedWrapper.id]
+ this.networkHandler.activeNetwork.selectedWrapper.expression = this.networkHandler.activeNetwork.expressionMap[this.networkHandler.activeNetwork.selectedWrapper.id];
}
if (zoom) {
this.zoomToNode(item.id);
@@ -490,7 +499,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
border: group.color,
background: group.color
}
- }
+ };
}
// if image is given, set node shape to image
if (group.image) {
@@ -539,9 +548,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
// nodes in selection have drugstoneId
const queryString = this.analysis.getSelection()
.filter(wrapper => wrapper.data.drugstoneType === 'protein')
- .map(wrapper => wrapper.data.uniprotAc)
+ .map(wrapper => wrapper.data.id)
.join('%0A');
- return 'http://biit.cs.ut.ee/gprofiler/gost?' +
+ return 'https://biit.cs.ut.ee/gprofiler/gost?' +
'organism=hsapiens&' +
`query=${queryString}&` +
'ordered=false&' +
@@ -557,19 +566,44 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
'background=';
}
+ openExternal(url) {
+ window.open(url, '_blank').focus();
+ }
+
+ async openDigest() {
+ let proteins = this.analysis.getSelection()
+ .filter(wrapper => wrapper.data.drugstoneType === 'protein')
+ .map(wrapper => wrapper.data.id);
+ let params = {
+ runs: 1000,
+ replace: 100,
+ distance: 'jaccard',
+ background_model: 'complete',
+ type: 'gene',
+ target: proteins,
+ target_id: this.drugstoneConfig.config.identifier
+ };
+
+ let resp = await this.netex.digest_request(params).catch(err => console.error(err));
+ let url = 'https://digest-validation.net/result?id=' + resp.task;
+ this.openExternal(url)
+ }
+
//TODO change to access through network service
@ViewChild('analysisPanel') analysisPanel;
getNodes(): any {
- if (this.selectedAnalysisToken && this.analysisPanel)
- return this.analysisPanel.getResultNodes()
+ if (this.selectedAnalysisToken && this.analysisPanel) {
+ return this.analysisPanel.getResultNodes();
+ }
return this.networkHandler.activeNetwork.inputNetwork.nodes;
}
getEdges(): any {
- if (this.selectedAnalysisToken && this.analysisPanel)
- return this.analysisPanel.getResultEdges()
- return this.networkHandler.activeNetwork.inputNetwork.edges
+ if (this.selectedAnalysisToken && this.analysisPanel) {
+ return this.analysisPanel.getResultEdges();
+ }
+ return this.networkHandler.activeNetwork.inputNetwork.edges;
}
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index de49c7b14fae14251b32c5dc46c08723faa08936..f4aa4e376735538b5d78c333cd589fe3c79bc7f5 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -43,6 +43,10 @@ export class NetexControllerService {
return this.http.get<Tissue[]>(`${environment.backend}tissues/`);
}
+ public digest_request(payload): Promise<any> {
+ return this.http.post('https://api.digest-validation.net/set', payload).toPromise();
+ }
+
public tissueExpressionGenes(tissue: Tissue, nodes: Node[]): Observable<any> {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
@@ -58,9 +62,9 @@ export class NetexControllerService {
public adjacentDisorders(nodes: Node[], nodeType: string, dataset: string, licenced: boolean): Observable<any> {
const params = {dataset: dataset, licenced: licenced};
if (nodeType === 'proteins') {
- params["proteins"] = nodes.filter((node: Node) => node.drugstoneId && node.drugstoneType === 'protein').flatMap((node: Node) => node.drugstoneId).map(id => id.slice(1));
+ params['proteins'] = nodes.filter((node: Node) => node.drugstoneId && node.drugstoneType === 'protein').flatMap((node: Node) => node.drugstoneId).map(id => id.slice(1));
} else if (nodeType === 'drugs') {
- params["drugs"] = nodes.map((node: Node) => node.drugId && node.drugstoneType === 'drug' ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
+ params['drugs'] = nodes.map((node: Node) => node.drugId && node.drugstoneType === 'drug' ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
}
return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
}
diff --git a/src/index.html b/src/index.html
index 38fc30b17b1964573c89e0e38ad6e39145b16cf2..010017586642ed624a07f95c7ee1d39110b63f2f 100644
--- a/src/index.html
+++ b/src/index.html
@@ -5,7 +5,7 @@
<title>Network Expander</title>
<base href="/">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <script type="text/javascript" src="https://unpkg.com/vis-network/standalone/umd/vis-network.min.js"></script>
+ <script type="text/javascript" src="http://unpkg.com/vis-network/standalone/umd/vis-network.min.js"></script>
<!-- <link rel="stylesheet" type="text/css" href="./stylesheets/default-theme.css">-->
</head>