diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 553ba0a6f9983687d7a1b46c5cafa24857b1c340..2de28df86dd706a710b466e30752892a684b2080 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -256,9 +256,9 @@
ID
<p-sortIcon [field]="'drugId'"></p-sortIcon>
</th>
- <th [pSortableColumn]="'name'">
- Name
- <p-sortIcon [field]="'name'"></p-sortIcon>
+ <th [pSortableColumn]="'label'">
+ Label
+ <p-sortIcon [field]="'label'"></p-sortIcon>
</th>
<th [pSortableColumn]="'status'">
Approved
@@ -285,7 +285,7 @@
<ng-template pTemplate="body" let-e>
<tr>
<td><a href="https://www.drugbank.ca/drugs/{{ e.drugId }}" target="_blank">{{ e.drugId }}</a></td>
- <td>{{e.name}}</td>
+ <td>{{e.label}}</td>
<td>
<span *ngIf="e.status === 'approved'">
<i class="fa fa-check"></i>
@@ -340,9 +340,9 @@
UniProt Code
<p-sortIcon [field]="'uniprotAc'"></p-sortIcon>
</th>
- <th [pSortableColumn]="'name'">
- Gene
- <p-sortIcon [field]="'name'"></p-sortIcon>
+ <th [pSortableColumn]="'symbol'">
+ Symbol
+ <p-sortIcon [field]="'symbol'"></p-sortIcon>
</th>
<th [pSortableColumn]="'proteinName'">
Name
@@ -368,7 +368,7 @@
<p-tableCheckbox [value]="e"></p-tableCheckbox>
</td>
<td><a href="https://www.uniprot.org/uniprot/{{ e.uniprotAc }}" target="_blank">{{ e.uniprotAc }}</a></td>
- <td>{{e.name}}</td>
+ <td>{{e.symbol}}</td>
<td>{{e.proteinName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
<td>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 8327f8a0a3ee6e598806e0a63b0ff86583193706..24b6ea5651e06310424c0ca213879f41d52c159f 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -33,6 +33,7 @@ import {NetworkSettings} from '../../network-settings';
import { NetexControllerService } from 'src/app/services/netex-controller/netex-controller.service';
import { IConfig } from 'src/app/config';
import { config } from 'rxjs';
+import { wrapReference } from '@angular/compiler/src/render3/util';
declare var vis: any;
@@ -387,6 +388,26 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
}
+ public inferNodeLabel(config: IConfig, wrapper: Wrapper): string {
+ if (wrapper.data.label) {
+ return wrapper.data.label;
+ }
+ const identifier = config.identifier;
+ if (identifier === 'uniprot'){
+ return wrapper.data.uniprotAc;
+ } else if (identifier === 'symbol') {
+ return wrapper.data.symbol;
+ } else if (identifier === 'ensg') {
+ // heuristc to find most important ensg is to look for smallest id
+ // parse ensg numbers to integers
+ const ensg_numbers = wrapper.data.ensg.map(x => parseInt(x));
+ // get index of smalles number
+ const i = ensg_numbers.reduce((iMin, x, i, arr) => x < arr[iMin] ? i : iMin, 0);
+ // return ensg-ID
+ return wrapper.data.ensg[i];
+ }
+ }
+
/**
* Maps analysis result returned from database to valid Vis.js network input
@@ -411,6 +432,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const scores = attributes.scores || {};
const details = attributes.details || {};
const wrappers: { [key: string]: Wrapper } = {};
+
for (const node of network.nodes) {
// backend converts object keys to PascalCase: p_123 --> p123
const nodeObjectKey = node.split('_').join('');
@@ -438,6 +460,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
};
}
+ /**
+ * maps node object returned from backend to frontend node, i.e. input to vis.js
+ * @param config
+ * @param wrapper
+ * @param isSeed
+ * @param score
+ * @returns
+ */
private mapNode(config: IConfig, wrapper: Wrapper, isSeed?: boolean, score?: number): any {
// const node = NetworkSettings.getNodeStyle(nodeType, isSeed, this.analysis.inSelection(wrapper));
let group = this.inferNodeGroup(wrapper);
@@ -446,7 +476,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
const node = JSON.parse(JSON.stringify(config.nodeGroups[group]));
node.id = wrapper.id;
- node.label = wrapper.data.symbol;
+ node.label = this.inferNodeLabel(config, wrapper);
node.nodeType = group;
node.isSeed = isSeed;
node.wrapper = wrapper;
diff --git a/src/app/config.ts b/src/app/config.ts
index b24458bb037e4466807ab082dd2858cf079f4bc3..efa5056de1ca3f4f0e0f31486692bb411090494b 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -19,7 +19,7 @@ export interface EdgeGroup {
color: string;
}
-export type Identifier = 'hugo'|'uniprot'|'ensg';
+export type Identifier = 'symbol'|'uniprot'|'ensg';
export type InteractionDrugProteinDB = 'DrugBank'|'Chembl'|'DGIdb';
export type InteractionProteinProteinDB = 'STRING'|'BioGRID'|'APID';
@@ -70,7 +70,7 @@ export const defaultConfig: IConfig = {
showTasks: true,
showFooter: true,
showLegend: true,
- identifier: 'hugo',
+ identifier: 'symbol',
interactionDrugProtein: 'DrugBank',
interactionProteinProtein: 'STRING',
nodeGroups: {
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 4faf19c9f2e4529f2cf9aecb790c7d832e66fa59..bbf91fa33a4d4d6fa489a57c231ae99adce54686 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -102,8 +102,14 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
public async startTask() {
+ // filter out all seed nodes that do not have a netex_Id, hence do not
+ // exist in the backend
+ const seeds = this.analysis.getSelection().map((item) => item.data.netexId)
+ const seedsFiltered = seeds.filter(function (el) {
+ return el != null;
+ });
const parameters: any = {
- seeds: this.analysis.getSelection().map((item) => item.data.netexId),
+ seeds: seedsFiltered,
config: this.config,
input_network: this.inputNetwork
};
@@ -117,7 +123,6 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
this.inputNetwork.nodes.forEach(node => {
delete node.interactions
});
- console.log(this.inputNetwork)
if (this.algorithm === 'trustrank') {
parameters.damping_factor = this.trustrankDampingFactor;
@@ -170,7 +175,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
parameters.hub_penalty = this.multisteinerHubPenalty;
}
+ console.log('parameters')
+ console.log(parameters)
await this.analysis.startAnalysis(this.algorithm, this.target, parameters);
}
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 56f660733c3945bd12922b1dcd8803f44b8ec997..0776354581ff56a88fb41150e974c0a499944e26 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -1,7 +1,7 @@
import {AlgorithmType, QuickAlgorithmType} from './services/analysis/analysis.service';
export interface Node {
- name: string;
+ label: string;
symbol: string;
id: string;
netexId?: string;
@@ -14,7 +14,6 @@ export interface Node {
x?: number;
y?: number;
expressionLevel?: number;
- label?: string;
}
export interface Tissue {
@@ -121,6 +120,8 @@ export function getWrapperFromCustom(gene: Node): Wrapper {
/**
* Constructs wrapper interface for gene
*/
+ // if gene.label is undefined, set it to id
+ gene.label = gene.label ? gene.label : gene.id
return {
id: getNodeId(gene),
nodeId: getNodeId(gene),
@@ -163,7 +164,7 @@ export interface Wrapper {
type: WrapperType;
data: {
id: string;
- name: string;
+ label: string;
symbol?: string;
netexId?: string;
ensg?: Array<string>;
@@ -172,7 +173,6 @@ export interface Wrapper {
interactions?: any;
group?: string;
uniprotAc?: string;
- label?: string;
expressionLevel?: number;
x?: number;
y?: number;
@@ -186,7 +186,7 @@ export interface Wrapper {
export interface Drug {
id: string;
- name: string;
+ label: string;
status: 'approved' | 'investigational';
inTrial: boolean;
inLiterature: boolean;
diff --git a/src/app/services/omnipath-controller/omnipath-controller.service.ts b/src/app/services/omnipath-controller/omnipath-controller.service.ts
index e86fa86c404b843fa02587c739eed7f7383f0835..4fe4d14c16bf627487b43093ad9a75fefd05cb94 100644
--- a/src/app/services/omnipath-controller/omnipath-controller.service.ts
+++ b/src/app/services/omnipath-controller/omnipath-controller.service.ts
@@ -34,7 +34,7 @@ export class OmnipathControllerService {
// entry 1 is always source uniprot ID, entry 2 always target uniprot ID
source = lineValues[0];
target = lineValues[1];
- } else if (identifier === 'hugo') {
+ } else if (identifier === 'symbol') {
// entry 3 is always source name, entry 4 always target name
source = lineValues[2];
target = lineValues[3];
diff --git a/src/index.html b/src/index.html
index f8606382ed84869563486d49a49286edd34be947..15df6aafbe35e3361391d8cf039524079863257b 100644
--- a/src/index.html
+++ b/src/index.html
@@ -38,13 +38,13 @@
<network-expander id="netexp1"
config='{
- "nodeGroups": {"0.5": {"type": "gene", "color": "rgb(204, 255, 51)", "name": "0.5", "shape": "circle"}, "1.5": {"type": "gene", "color": "rgb(102, 255, 51)", "name": "1.5", "shape": "circle"}, "2.0": {"type": "gene", "color": "rgb(51, 204, 51)", "name": "2.0", "shape": "circle"}, "-2.0": {"type": "gene", "color": "rgb(255, 0, 0)", "name": "-2.0", "shape": "circle"}},
+ "nodeGroups": {"0.5": {"type": "gene", "color": "rgb(204, 255, 51)", "name": "0.5", "shape": "circle"}, "patient_group": {"type": "patient", "color": "red", "name": "patient group", "shape": "circle"}, "2.0": {"type": "gene", "color": "rgb(51, 204, 51)", "name": "2.0", "shape": "circle"}, "-2.0": {"type": "gene", "color": "rgb(255, 0, 0)", "name": "-2.0", "shape": "circle"}},
"edgeGroups": {"custom": {"color": "black", "name": "Custom Group"}},
- "identifier": "ensg",
+ "identifier": "symbol",
"legendUrl": "https://exbio.wzw.tum.de/covex/assets/leg1.png"
}'
network='{
- "nodes": [{"id": "ENSG00000171862", "group": "0.5"}, {"label": "ENSG00000284792", "id": "ENSG00000284792", "group": 0.5}],
+ "nodes": [{"id": "TP53", "group": "0.5"}, {"id": "C5", "group": "0.5"}, {"id": "Patient", "group": "patient_group"}, {"label": "PTEN", "id": "PTEN", "group": 0.5}],
"edges": []
}'
style="height: 100%; width: 100vw; display: block;"