display drugs and nodes in analysis network; display custom nodes like...

display drugs and nodes in analysis network; display custom nodes like patients; TODO: node type is not passed on from group AND node style in analysis is not loaded correctly, falls back to default.+

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>

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;

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: {

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);
   }
 

src/app/interfaces.ts

 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;

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];

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;"