diff --git a/src/app/analysis.service.ts b/src/app/analysis.service.ts
index 0a94fbbb80ae71bc388bf46105b5069fb31abb9d..a1a2b97dbe0328636e028324ddd19cf155aefd6c 100644
--- a/src/app/analysis.service.ts
+++ b/src/app/analysis.service.ts
@@ -5,7 +5,7 @@ import {environment} from '../environments/environment';
import {toast} from 'bulma-toast';
import {Injectable} from '@angular/core';
-export type AlgorithmType = 'trustrank' | 'keypathwayminer' | 'multisteiner' | 'closeness' | 'degree' | 'proximity';
+export type AlgorithmType = 'trustrank' | 'keypathwayminer' | 'multisteiner' | 'closeness' | 'degree' | 'proximity' | 'betweenness';
export type QuickAlgorithmType = 'quick' | 'super';
export const algorithmNames = {
@@ -15,6 +15,7 @@ export const algorithmNames = {
closeness: 'Closeness Centrality',
degree: 'Degree Centrality',
proximity: 'Network Proximity',
+ betweenness: 'Betweenness Centrality',
quick: 'Simple',
super: 'Quick-Start',
};
@@ -28,6 +29,7 @@ export const TRUSTRANK: Algorithm = {slug: 'trustrank', name: algorithmNames.tru
export const CLOSENESS_CENTRALITY: Algorithm = {slug: 'closeness', name: algorithmNames.closeness};
export const DEGREE_CENTRALITY: Algorithm = {slug: 'degree', name: algorithmNames.degree};
export const NETWORK_PROXIMITY: Algorithm = {slug: 'proximity', name: algorithmNames.proximity};
+export const BETWEENNESS_CENTRALITY: Algorithm = {slug: 'betweenness', name: algorithmNames.betweenness};
export const KEYPATHWAYMINER: Algorithm = {slug: 'keypathwayminer', name: algorithmNames.keypathwayminer};
export const MULTISTEINER: Algorithm = {slug: 'multisteiner', name: algorithmNames.multisteiner};
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index dfc224ea4f41482d795864bfa473218ddc7eae81..1f577b9f405fec8399734af4621591ba01c596b7 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -60,7 +60,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
@Output() tokenChange = new EventEmitter<string | null>();
@Output() showDetailsChange = new EventEmitter<Wrapper>();
- @Output() visibleItems = new EventEmitter<[any[], [Protein[], ViralProtein[], Drug[]]]>();
+ @Output() visibleItems = new EventEmitter<[any[], [Protein[], ViralProtein[], Tissue]]>();
public task: Task | null = null;
@@ -332,7 +332,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public emitVisibleItems(on: boolean) {
if (on) {
- this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.effects, []]]);
+ this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.effects, this.selectedTissue]]);
} else {
this.visibleItems.emit(null);
}
@@ -651,44 +651,42 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
- return;
- }
-
- this.selectedTissue = tissue;
-
- const minExp = 0.3;
-
- this.http.get<Array<{ protein: Protein, level: number }>>(
- `${environment.backend}tissue_expression/?tissue=${tissue.id}&token=${this.token}`)
- .subscribe((levels) => {
- const updatedNodes = [];
- const maxExpr = Math.max(...levels.map(lvl => lvl.level));
- for (const lvl of levels) {
- const item = getWrapperFromProtein(lvl.protein);
- const node = this.nodeData.nodes.get(item.nodeId);
- if (!node) {
- continue;
+ } else {
+ this.selectedTissue = tissue;
+ const minExp = 0.3;
+ this.http.get<Array<{ protein: Protein, level: number }>>(
+ `${environment.backend}tissue_expression/?tissue=${tissue.id}&token=${this.token}`)
+ .subscribe((levels) => {
+ const updatedNodes = [];
+ const maxExpr = Math.max(...levels.map(lvl => lvl.level));
+ for (const lvl of levels) {
+ const item = getWrapperFromProtein(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);
}
- 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.nodeData.nodes.update(updatedNodes);
+ });
+ }
+ this.emitVisibleItems(true);
}
}
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 8dbaf9d91da581e9734c131bf687be224dd658c4..abc58f66a7223697bed45c3ac9124236bb2a6c51 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -55,6 +55,7 @@
<div *ngFor="let link of wrapper.data.trialLinks" class="list-item">
<a [href]="link" target="_blank">{{beautify(link)}}</a>
</div>
+ <small class="list-item"><i>Links provided by WHO</i></small>
</div>
</div>
diff --git a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.html b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.html
index 9cf4f5dc7af8a1a704adb6e601bcfcfec329f8b5..47e9217dcffca4afd5a63bcb207adc381f6680cf 100644
--- a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.html
+++ b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.html
@@ -4,31 +4,56 @@
<header class="modal-card-head">
<p class="modal-card-title">
<span class="icon"><i class="fa fa-dna"></i></span>
- Add Expressed Proteins
+ Add Tissue Proteins
</p>
<button (click)="close()" class="delete" aria-label="close"></button>
</header>
<section class="modal-card-body">
- <div class="field">
- <label class="label" for="threshold">Threshold</label>
+ <div class="notification is-warning" *ngIf="addedCount === 0">
+ No host proteins have been selected or added.
+ </div>
+ <div class="notification is-warning" *ngIf="addedCount > 0">
+ {{addedCount}} host proteins have been selected or added.
+ </div>
+ <p *ngIf="!selectedTissue">
+ <i>
+ In order to add proteins expressed in specific tissues,
+ please select a tissue in the main network window to the bottom.
+ </i>
+ </p>
+ <p *ngIf="selectedTissue" class="mb-3">
+ Currently selected tissue: <strong>{{selectedTissue.name}}</strong>
+ </p>
+ <div class="field" *ngIf="selectedTissue">
+ <label class="label" for="threshold">Threshold (TPM)</label>
<div class="control">
<input [ngModel]="threshold" (ngModelChange)="setThreshold($event)" id="threshold" class="input" type="number"
placeholder="Threshold" required>
</div>
<p class="help">
- All proteins above this threshold.
+ All proteins above this threshold in transcripts per million (TPM) will be added or selected.
</p>
</div>
</section>
<footer class="modal-card-foot">
+ <button (click)="addProteins();" class="button is-success is-rounded has-tooltip"
+ data-tooltip="Add all to the selection."
+ [disabled]="proteins.length === 0 || !selectedTissue || loading">
+ <span class="icon">
+ <i class="fas fa-plus"></i>
+ </span>
+ <span>
+ Add proteins
+ </span>
+ </button>
<button (click)="addVisibleProteins();" class="button is-success is-rounded has-tooltip"
data-tooltip="Add to selection if they appear in the current network."
- [disabled]="proteins.length === 0">
+ [disabled]="proteins.length === 0 || !selectedTissue || loading">
<span class="icon">
<i class="fas fa-expand"></i>
</span>
<span>
- Select {{proteins.length}} proteins
+ Select proteins ({{proteins.length}})
</span>
</button>
<button (click)="close()" class="button is-rounded has-tooltip" data-tooltip="Close the current window.">
diff --git a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
index 9b9bf3060ed1332a0480b6a5e6138b1e2a317141..6b9e198705199d78463c8278e166f904a1126034 100644
--- a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
+++ b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
@@ -1,6 +1,8 @@
import {Component, EventEmitter, Input, OnChanges, Output, SimpleChanges} from '@angular/core';
import {AnalysisService} from '../../analysis.service';
-import {Protein} from '../../interfaces';
+import {getWrapperFromProtein, Protein, Tissue} from '../../interfaces';
+import {environment} from '../../../environments/environment';
+import {HttpClient} from '@angular/common/http';
@Component({
selector: 'app-add-expressed-proteins',
@@ -17,21 +19,37 @@ export class AddExpressedProteinsComponent implements OnChanges {
public visibleNodes: Array<any> = [];
@Input()
public currentViewProteins: Array<Protein> = [];
+ @Input()
+ public selectedTissue: Tissue | null = null;
public proteins = [];
-
public threshold = 5;
+ public addedCount: number | null = null;
+ public loading = false;
- constructor(private analysis: AnalysisService) {
+ constructor(private http: HttpClient, private analysis: AnalysisService) {
}
- public close() {
- this.show = false;
- this.showChange.emit(this.show);
+ ngOnChanges(changes: SimpleChanges): void {
+ this.setThreshold(this.threshold);
+ }
+
+ public async addProteins() {
+ this.loading = true;
+ const result = await this.http.post<any>(`${environment.backend}query_tissue_proteins/`,
+ {tissueId: this.selectedTissue.id, threshold: this.threshold}).toPromise();
+ const items = [];
+ for (const detail of result) {
+ items.push(getWrapperFromProtein(detail));
+ }
+ this.addedCount = this.analysis.addItems(items);
+ this.loading = false;
}
public addVisibleProteins() {
- this.analysis.addExpressedHostProteins(this.visibleNodes, this.currentViewProteins, this.threshold);
+ this.loading = true;
+ this.addedCount = this.analysis.addExpressedHostProteins(this.visibleNodes, this.currentViewProteins, this.threshold);
+ this.loading = false;
}
public setThreshold(threshold: number) {
@@ -42,8 +60,10 @@ export class AddExpressedProteinsComponent implements OnChanges {
this.proteins = this.currentViewProteins.filter(p => p.expressionLevel >= threshold);
}
- ngOnChanges(changes: SimpleChanges): void {
- this.setThreshold(this.threshold);
+ public close() {
+ this.show = false;
+ this.showChange.emit(this.show);
+ this.addedCount = null;
}
}
diff --git a/src/app/dialogs/custom-proteins/custom-proteins.component.html b/src/app/dialogs/custom-proteins/custom-proteins.component.html
index 7eb960a1bf9bed70ea79ffa99e8feada0e9e8828..4b9dbad6562df7eb3d5f9617dcf67fa06d4baa27 100644
--- a/src/app/dialogs/custom-proteins/custom-proteins.component.html
+++ b/src/app/dialogs/custom-proteins/custom-proteins.component.html
@@ -44,7 +44,7 @@
<footer class="modal-card-foot">
<button (click)="addProteins();" class="button is-success is-rounded has-tooltip"
data-tooltip="Add all to the selection."
- [disabled]="proteins.length === 0">
+ [disabled]="proteins.length === 0 || loading">
<span class="icon">
<i class="fa fa-plus"></i>
</span>
@@ -54,7 +54,7 @@
</button>
<button (click)="addVisibleProteins();" class="button is-success is-rounded has-tooltip"
data-tooltip="Add to selection if they appear in the current network."
- [disabled]="proteins.length === 0">
+ [disabled]="proteins.length === 0 || loading">
<span class="icon">
<i class="fas fa-expand"></i>
</span>
diff --git a/src/app/dialogs/custom-proteins/custom-proteins.component.ts b/src/app/dialogs/custom-proteins/custom-proteins.component.ts
index 55bb13ddedb789d650c87f576e0eb41288ac5ff3..a6994260cddbaba0302cadec4b03dfa1fd9cc1fa 100644
--- a/src/app/dialogs/custom-proteins/custom-proteins.component.ts
+++ b/src/app/dialogs/custom-proteins/custom-proteins.component.ts
@@ -24,6 +24,7 @@ export class CustomProteinsComponent implements OnInit {
public itemsFound: Array<Wrapper> = [];
public addedCount = 0;
public selectOnly = false;
+ public loading = false;
constructor(private http: HttpClient, private analysis: AnalysisService) { }
@@ -42,6 +43,7 @@ export class CustomProteinsComponent implements OnInit {
}
public async addProteins() {
+ this.loading = true;
this.notFound = [];
this.itemsFound = [];
const proteins = this.proteins;
@@ -56,9 +58,11 @@ export class CustomProteinsComponent implements OnInit {
this.itemsFound = items;
this.addedCount = this.analysis.addItems(items);
this.selectOnly = false;
+ this.loading = false;
}
public async addVisibleProteins() {
+ this.loading = true;
this.notFound = [];
this.itemsFound = [];
const proteins = this.proteins;
@@ -75,6 +79,7 @@ export class CustomProteinsComponent implements OnInit {
this.itemsFound = items;
this.addedCount = this.analysis.addVisibleHostProteins(this.visibleNodes, proteinItems);
this.selectOnly = true;
+ this.loading = false;
}
public changeTextList(textList) {
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index df64a9f1cb9ed2d0a64b6da3c217a9aa9d36084b..25154731e1ee3180e52b33d52f3d2e442ab81d3a 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -115,9 +115,13 @@
<div class="content">
<h6 class="is-6">About TrustRank</h6>
<p>
- <a href="https://en.wikipedia.org/wiki/TrustRank" target="_blank">TrustRank</a>
- is a node centrality measure that ranks nodes in a network based on how well they are connected to a
- (trusted) set of seed nodes (Gyöngyi, Garcia-Molina, and Pedersen 2004).
+ TrustRank is a node centrality measure that ranks nodes in a network based on how well they are
+ connected to a (trusted) set of seed nodes.
+ </p>
+ <p>
+ <a href="https://docs.google.com/document/d/1_SRnIx_UC8FR59rMyrf_r45fCIt3naP4t1qefYNp9vk" target="_blank">
+ Check the documentation for more info
+ </a>
</p>
</div>
</div>
@@ -194,9 +198,8 @@
<div class="content">
<h6 class="is-6">About Closeness Centrality</h6>
<p>
- <a href="https://en.wikipedia.org/wiki/Closeness_centrality" target="_blank">Closeness Centrality</a>
- is a node centrality measure that ranks the nodes in a network based on the lengths of their shortest
- paths to all other nodes in the network (Kaczprowski, Doncheva, and Albrecht 2013).
+ Closeness Centrality is a node centrality measure that ranks the nodes in a network based on the
+ lengths of their shortest paths to all other nodes in the network.
</p>
</div>
</div>
@@ -250,11 +253,8 @@
<div class="content">
<h6 class="is-6">About Degree Centrality</h6>
<p>
- <a href="https://en.wikipedia.org/wiki/Centrality#Degree_centrality" target="_blank">
- Degree Centrality
- </a>
- assigns an importance score based simply on the number of links held by each node. In CoVex, we use
- a modified version which does not consider all links but only the neighbouring seeds.
+ Degree Centrality assigns an importance score based simply on the number of links held by each node.
+ In CoVex, we use a modified version which does not consider all links but only the neighbouring seeds.
</p>
</div>
</div>
@@ -280,28 +280,6 @@
[(value)]="proximityIncludeNonApprovedDrugs"></app-toggle>
</div>
- <div class="field">
- <label class="label" for="proximity-rss">No. of random seed sets</label>
- <div class="control">
- <input [(ngModel)]="proximityNumRandomSeedSets" id="proximity-rss" class="input" type="number"
- placeholder="Maximum degree" min="0" max="1" required>
- </div>
- <p class="help">
- Number of random seed sets for computing Z-scores.
- </p>
- </div>
-
- <div class="field">
- <label class="label" for="proximity-rdts">No. of random drug target sets</label>
- <div class="control">
- <input [(ngModel)]="proximityNumRandomDrugTargetSets" id="proximity-rdts" class="input" type="number"
- placeholder="Maximum degree" min="0" max="1" required>
- </div>
- <p class="help">
- Number of random drug target sets for computing Z-scores.
- </p>
- </div>
-
<div class="field">
<label class="label" for="proximity-md">Maximum degree</label>
<div class="control">
@@ -324,6 +302,52 @@
</p>
</div>
+ <div class="box">
+ <article class="media">
+ <div class="media-left">
+ <span class="icon"><i class="fa fa-info"></i></span>
+ </div>
+ <div class="media-content">
+ <div class="content">
+ <h6 class="is-6">About Degree Centrality</h6>
+ <p>
+ Degree Centrality uses the average minimum distance from the drug’s targets to all of the selected
+ seeds as a measure of proximity.
+ </p>
+ </div>
+ </div>
+ </article>
+ </div>
+
+ </div>
+
+ <div *ngIf="algorithm==='betweenness'">
+
+ <div class="field">
+ <label class="label" for="proximity-rs">Result size</label>
+ <div class="control">
+ <input [(ngModel)]="betweennessResultSize" id="betweenness-rs" class="input" type="number"
+ placeholder="Result size" required>
+ </div>
+ </div>
+
+ <div class="box">
+ <article class="media">
+ <div class="media-left">
+ <span class="icon"><i class="fa fa-info"></i></span>
+ </div>
+ <div class="media-content">
+ <div class="content">
+ <h6 class="is-6">About Betweenness Centrality</h6>
+ <p>
+ Betweenness Centrality ranks the proteins in a network based on how many shortest paths pass through
+ them.
+ </p>
+ </div>
+ </div>
+ </article>
+ </div>
+
</div>
<div *ngIf="algorithm==='keypathwayminer'">
@@ -367,9 +391,8 @@
<div class="content">
<h6 class="is-6">About KeyPathwayMiner</h6>
<p>
- <a href="https://keypathwayminer.compbio.sdu.dk/keypathwayminer/">KeyPathwayMiner</a>
- is a network enrichment tool that identifies condition-specific sub-networks (key pathways)
- (Alcaraz et al. 2016).
+ KeyPathwayMiner is a network enrichment tool that identifies condition-specific sub-networks
+ (key pathways) (Alcaraz et al. 2016).
</p>
</div>
</div>
@@ -446,25 +469,13 @@
[(value)]="multisteinerIncludeViralNonSeeds"></app-toggle>
</div>
- <div class="box">
- <article class="media">
- <div class="media-left">
- <span class="icon"><i class="fa fa-info"></i></span>
- </div>
- <div class="media-content">
- <div class="content">
- <h6 class="is-6">About Multi-Steiner</h6>
- <p>
- The <a href="https://en.wikipedia.org/wiki/Steiner_tree_problem">Steiner tree</a>
- problem is a classical combinatorial optimization problem. It asks to find a sub-graph
- of minimum size connecting a given set of seed nodes.
- </p>
- </div>
- </div>
- </article>
- </div>
-
</div>
+
+ <p class="doc-link">
+ <a href="https://docs.google.com/document/d/1_SRnIx_UC8FR59rMyrf_r45fCIt3naP4t1qefYNp9vk" target="_blank">
+ Check the documentation for more info
+ </a>
+ </p>
</section>
<footer class="modal-card-foot">
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.scss b/src/app/dialogs/launch-analysis/launch-analysis.component.scss
index 07fa0d31e0d3f77829ed228285185c1cbe457022..717dbc6cc5486f837779e6c85e938b9773aa77ba 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.scss
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.scss
@@ -19,3 +19,8 @@
background-color: blue;
}
}
+
+.doc-link {
+ margin-top: 15px;
+ font-size: 11px;
+}
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 285d84158a938bcc1de89ffa3bb42eb753e4af4b..640fc9095d631b6ab8b7611637a640b51ad17eb5 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -2,7 +2,7 @@ import {Component, EventEmitter, Input, OnChanges, OnInit, Output, SimpleChanges
import {
Algorithm,
AlgorithmType,
- AnalysisService, CLOSENESS_CENTRALITY,
+ AnalysisService, BETWEENNESS_CENTRALITY, CLOSENESS_CENTRALITY,
DEGREE_CENTRALITY,
KEYPATHWAYMINER, MAX_TASKS,
MULTISTEINER, NETWORK_PROXIMITY,
@@ -58,10 +58,11 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public proximityIncludeNonApprovedDrugs = false;
public proximityMaxDeg = 0;
public proximityHubPenalty = 0.0;
- public proximityNumRandomSeedSets = 32;
- public proximityNumRandomDrugTargetSets = 32;
public proximityResultSize = 20;
+ // Betweenness Parameters
+ public betweennessResultSize = 20;
+
// Keypathwayminer Parameters
public keypathwayminerK = 5;
@@ -88,7 +89,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
ngOnChanges(changes: SimpleChanges): void {
if (this.target === 'drug-target') {
- this.algorithms = [MULTISTEINER, KEYPATHWAYMINER, TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY];
+ this.algorithms = [MULTISTEINER, KEYPATHWAYMINER, TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY, BETWEENNESS_CENTRALITY];
this.algorithm = MULTISTEINER.slug;
} else if (this.target === 'drug') {
this.algorithms = [TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY, NETWORK_PROXIMITY];
@@ -141,9 +142,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.max_deg = this.proximityMaxDeg;
}
parameters.hub_penalty = this.proximityHubPenalty;
- parameters.num_random_seed_sets = this.proximityNumRandomSeedSets;
- parameters.num_random_drug_target_sets = this.proximityNumRandomDrugTargetSets;
parameters.result_size = this.proximityResultSize;
+ } else if (this.algorithm === 'betweenness') {
+ parameters.result_size = this.betweennessResultSize;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
} else if (this.algorithm === 'multisteiner') {
diff --git a/src/app/pages/about-page/about-page.component.html b/src/app/pages/about-page/about-page.component.html
index 06ad3b90b58fcfb645c1ff5fb2ce2dbc1ac62474..a0732b1fcd669f8c098a5260eee234b8a54b12ef 100644
--- a/src/app/pages/about-page/about-page.component.html
+++ b/src/app/pages/about-page/about-page.component.html
@@ -19,15 +19,17 @@
<br>
CoVex (Coronavirus Explorer) is a unique online network and systems medicine platform for data analysis that
integrates virus-human interactions for SARS-CoV-2 and SARS-CoV-1. It implements different network-based
- approaches for the identification of new drug targets and new repurposable drugs.
+ approaches for the identification of new drug targets and new repurposable drugs.<br>
<br>
+ For instructions and help check the documentation:
+ <a href="https://docs.google.com/document/d/1_SRnIx_UC8FR59rMyrf_r45fCIt3naP4t1qefYNp9vk">CoVex Documentation</a><br>
+ <br>
+ For detailed information please visit our blog: <a href="https://www.exbio.de/exbio-vs-covid-part-1/">ExBio vs Covid</a><br>
<br>
- For detailed information please visit our blog: <a href="https://www.exbio.de/exbio-vs-covid-part-1/"> https://www.exbio.de/exbio-vs-covid-part-1/</a>
- <br>
- <br>
We are constantly updating and integrating new data as it becomes available.
- <br>
- If you are interested to make your virus-human interactome data available via our platform, please contact us.
+ <br>
+ If you are interested to make your virus-human interactome data available via our platform, please contact
+ us.
</p>
<h2 class="subtitle">General workflow of the platform</h2>
<ol>
@@ -48,7 +50,7 @@
<li>Systems and network medicine: Sepideh Sadegh (sadegh_AT_wzw.tum.de)</li>
<li>Web platform: Julian Matschinske (julian.matschinske_AT_wzw.tum.de)</li>
<li>Project coordination: Prof. Dr. Jan Baumbach (jan.baumbach_AT_wzw.tum.de)</li>
- <li>Lab website: <a href="http://www.exbio.de">http://www.exbio.de</a> </li>
+ <li>Lab website: <a href="http://www.exbio.de">http://www.exbio.de</a></li>
</ul>
<br>
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 81b06e2a7d08ac5e4ba62a9c6dd7e944a6187448..9118923b4b373df445a10e80f28584b70a6f429b 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -8,6 +8,7 @@
</app-custom-proteins>
<app-add-expressed-proteins [(show)]="showThresholdDialog"
+ [selectedTissue]="currentViewSelectedTissue"
[visibleNodes]="currentViewNodes"
[currentViewProteins]="currentViewProteins">
</app-add-expressed-proteins>
@@ -180,7 +181,8 @@
<div class="dropdown-trigger">
<button (click)="expressionExpanded=!expressionExpanded"
class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
- aria-haspopup="true" aria-controls="dropdown-menu">
+ aria-haspopup="true" aria-controls="dropdown-menu"
+ data-tooltip="Tissue expression data is provided by the GTEx project.">
<span *ngIf="!selectedTissue">Tissue</span>
<span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
<span class="icon is-small">
@@ -569,7 +571,7 @@
<i class="fa fa-angle-double-up"></i>
</span>
<span>
- Expressed proteins
+ Tissue proteins
</span>
</a>
</footer>
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index ce0a44c7348d75609b51e33ca32d56766a358910..85fa3ed0b02a05ba815cb779eeb6fc2c4b60aba5 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -69,6 +69,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public currentViewProteins: Protein[];
public currentViewViralProteins: ViralProtein[];
+ public currentViewSelectedTissue: Tissue | null = null;
public currentViewNodes: any[];
public expressionExpanded = false;
@@ -471,15 +472,17 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
}
- analysisWindowChanged($event: any) {
+ analysisWindowChanged($event: [any[], [Protein[], ViralProtein[], Tissue]]) {
if ($event) {
this.currentViewNodes = $event[0];
this.currentViewProteins = $event[1][0];
this.currentViewViralProteins = $event[1][1];
+ this.currentViewSelectedTissue = $event[1][2];
} else {
this.currentViewNodes = this.nodeData.nodes;
this.currentViewProteins = this.proteins;
this.currentViewViralProteins = this.effects;
+ this.currentViewSelectedTissue = this.selectedTissue;
}
}
@@ -505,6 +508,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
public selectTissue(tissue: Tissue | null) {
+ this.expressionExpanded = false;
if (!tissue) {
this.selectedTissue = null;
const updatedNodes = [];
@@ -532,45 +536,47 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
- return;
- }
-
- this.selectedTissue = tissue;
+ } else {
+ this.selectedTissue = tissue;
+
+ const minExp = 0.3;
+
+ const params = new HttpParams().set('tissue', `${tissue.id}`).set('data', JSON.stringify(this.currentDataset));
+ this.http.get<any>(
+ `${environment.backend}tissue_expression/`, {params})
+ .subscribe((levels) => {
+ const updatedNodes = [];
+ const maxExpr = Math.max(...levels.map(lvl => lvl.level));
+ for (const lvl of levels) {
+ const item = getWrapperFromProtein(lvl.protein);
+ const node = this.nodeData.nodes.get(item.nodeId);
+ if (!node) {
+ continue;
+ }
+ const gradient = lvl.level !== null ? (Math.pow(lvl.level / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
+ const pos = this.network.getPositions([item.nodeId]);
+ node.x = pos[item.nodeId].x;
+ node.y = pos[item.nodeId].y;
+ Object.assign(node,
+ NetworkSettings.getNodeStyle(
+ node.wrapper.type,
+ node.isSeed,
+ this.analysis.inSelection(item),
+ undefined,
+ undefined,
+ gradient));
+ node.wrapper = item;
+ node.gradient = gradient;
+ this.proteins.find(prot => getProteinNodeId(prot) === item.nodeId).expressionLevel = lvl.level;
+ (node.wrapper.data as Protein).expressionLevel = lvl.level;
+ updatedNodes.push(node);
+ }
+ this.nodeData.nodes.update(updatedNodes);
+ });
- const minExp = 0.3;
+ }
- const params = new HttpParams().set('tissue', `${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 = getWrapperFromProtein(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;
}
}
diff --git a/src/styles.scss b/src/styles.scss
index 8329e918f2ffda492864fb4c0d1b1b84d4a720e5..d2b730c504ac0769aa05422298e875e5a919e611 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -234,3 +234,7 @@ body {
padding-right: 5px;
}
}
+
+.mb-3 {
+ margin-bottom: 10px;
+}