diff --git a/src/app/analysis.service.ts b/src/app/analysis.service.ts
index aaf632bd7b32d92b3a99b5a843731a70e6411f36..7b274f49907765d1f5a82dafd5e4cdd28c20b77e 100644
--- a/src/app/analysis.service.ts
+++ b/src/app/analysis.service.ts
@@ -36,9 +36,13 @@ export const MAX_TASKS = 3;
})
export class AnalysisService {
+ private selection = 'main';
+
private selectedItems = new Map<string, Wrapper>();
private selectListSubject = new Subject<{ items: Wrapper[], selected: boolean | null }>();
+ private selections = new Map<string, Map<string, Wrapper>>();
+
public tokens: string[] = [];
public finishedTokens: string[] = [];
public tasks: Task[] = [];
@@ -52,7 +56,6 @@ export class AnalysisService {
const tokens = localStorage.getItem('tokens');
const finishedTokens = localStorage.getItem('finishedTokens');
-
if (tokens) {
this.tokens = JSON.parse(tokens);
}
@@ -82,6 +85,17 @@ export class AnalysisService {
});
}
+ public switchSelection(id: string) {
+ this.selections.set(this.selection, this.selectedItems);
+ if (this.selections.has(id)) {
+ this.selectedItems = this.selections.get(id);
+ } else {
+ this.selectedItems = new Map<string, Wrapper>();
+ }
+ this.selectListSubject.next({items: Array.from(this.selectedItems.values()), selected: null});
+ this.selection = id;
+ }
+
public addItems(wrappers: Wrapper[]): number {
const addedWrappers: Wrapper[] = [];
for (const wrapper of wrappers) {
@@ -104,6 +118,47 @@ export class AnalysisService {
this.selectListSubject.next({items: removedWrappers, selected: false});
}
+ public addSeeds(nodes) {
+ const addedWrappers: Wrapper[] = [];
+ nodes.forEach((node) => {
+ const wrapper: Wrapper = node.wrapper;
+ if (node.isSeed === true && !this.inSelection(wrapper)) {
+ addedWrappers.push(wrapper);
+ this.selectedItems.set(wrapper.nodeId, wrapper);
+ }
+ });
+ this.selectListSubject.next({items: addedWrappers, selected: true});
+ }
+
+ public removeSeeds(nodes) {
+ const removedWrappers: Wrapper[] = [];
+ nodes.forEach((node) => {
+ const wrapper: Wrapper = node.wrapper;
+ if (node.isSeed === true && this.inSelection(wrapper)) {
+ removedWrappers.push(wrapper);
+ this.selectedItems.delete(wrapper.nodeId);
+ }
+ });
+ this.selectListSubject.next({items: removedWrappers, selected: false});
+ }
+
+ public invertSelection(nodes) {
+ const newSelection = [];
+ nodes.forEach((node) => {
+ const wrapper: Wrapper = node.wrapper;
+ if (wrapper.type === 'host' || wrapper.type === 'virus') {
+ if (!this.inSelection(wrapper)) {
+ newSelection.push(wrapper);
+ }
+ }
+ });
+ this.selectedItems.clear();
+ for (const wrapper of newSelection) {
+ this.selectedItems.set(wrapper.nodeId, wrapper);
+ }
+ this.selectListSubject.next({items: newSelection, selected: null});
+ }
+
public addVisibleHostProteins(nodes, proteins): number {
const items: Wrapper[] = [];
const visibleIds = new Set<string>(nodes.getIds());
@@ -151,8 +206,8 @@ export class AnalysisService {
}
resetSelection() {
- this.selectListSubject.next({items: [], selected: null});
this.selectedItems.clear();
+ this.selectListSubject.next({items: [], selected: null});
}
idInSelection(nodeId: string): boolean {
diff --git a/src/app/app.component.html b/src/app/app.component.html
index 1197c795f5d8ff1ea8c4f7ce382b28f82354049b..0b629bc97d450992e426898145d6ff620da96d11 100644
--- a/src/app/app.component.html
+++ b/src/app/app.component.html
@@ -28,7 +28,7 @@
<div class="navbar-item">
<div class="field is-grouped">
<p class="control">
- Version 1.0
+ Version 1.1
</p>
</div>
</div>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 02cf7ec80e0f2f551e4f8e0ad57a1569fc57c90e..590ae7ca3b762912922917d3acbba848b438b9c4 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -93,19 +93,19 @@
</tr>
<tr>
<td>Tolerance</td>
- <td>10</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>Hub Penality</td>
+ <td>1</td>
</tr>
</tbody>
</table>
<p>
- Algorithm: <strong>{{algorithmNames['trustrank']}}</strong>
+ Algorithm: <strong>{{algorithmNames['closeness']}}</strong>
</p>
<table class="table is-narrow">
<tbody>
- <tr>
- <td>Damping Factor</td>
- <td>0.85</td>
- </tr>
<tr>
<td>Include indirect drugs</td>
<td>
@@ -115,12 +115,16 @@
<tr>
<td>Include non-approved drugs</td>
<td>
- <i class="fa fa-times"></i>
+ <i class="fa fa-check"></i>
</td>
</tr>
+ <tr>
+ <td>Hub Penality</td>
+ <td>1</td>
+ </tr>
<tr>
<td>Result Size</td>
- <td>30</td>
+ <td>10</td>
</tr>
</tbody>
</table>
@@ -228,17 +232,28 @@
<p-sortIcon [field]="'name'"></p-sortIcon>
</th>
<th [pSortableColumn]="'status'">
- Status
+ Approved
<p-sortIcon [field]="'status'"></p-sortIcon>
</th>
<th [pSortableColumn]="'inTrial'">
- Trial
+ In Trial
<p-sortIcon [field]="'inTrial'"></p-sortIcon>
</th>
+ <th [pSortableColumn]="'inLiterature'">
+ In Literature
+ <p-sortIcon [field]="'inLiterature'"></p-sortIcon>
+ </th>
<th *ngIf="tableHasScores" [pSortableColumn]="'score'">
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
+ <th>
+ Closest viral proteins
+ </th>
+ <th [pSortableColumn]="'closestDistance'">
+ Viral protein distance
+ <p-sortIcon [field]="'closestDistance'"></p-sortIcon>
+ </th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
@@ -248,20 +263,37 @@
<td>
<span *ngIf="e.status === 'approved'">
<i class="fa fa-check"></i>
- approved
+ Approved
</span>
<span *ngIf="e.status === 'unapproved'">
<i class="fa fa-times"></i>
- not approved
</span>
</td>
<td>
<span *ngIf="e.inTrial">
<i class="fa fa-microscope has-text-primary"></i>
- in Trial
+ Trial
+ </span>
+ <span *ngIf="!e.inTrial">
+ <i class="fa fa-times"></i>
+ </span>
+ </td>
+ <td>
+ <span *ngIf="e.inLiterature">
+ <i class="fa fa-book has-text-primary"></i>
+ Literature
+ </span>
+ <span *ngIf="!e.inLiterature">
+ <i class="fa fa-times"></i>
</span>
</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
+ <td title="{{previewStringArray(e.closestViralProteins, 100)}}">
+ {{previewStringArray(e.closestViralProteins, 3)}}
+ </td>
+ <td>
+ {{e.closestDistance}}
+ </td>
</tr>
</ng-template>
</p-table>
@@ -292,10 +324,25 @@
Gene
<p-sortIcon [field]="'name'"></p-sortIcon>
</th>
+ <th [pSortableColumn]="'proteinName'">
+ Name
+ <p-sortIcon [field]="'proteinName'"></p-sortIcon>
+ </th>
<th *ngIf="tableHasScores" [pSortableColumn]="'score'">
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
+ <th [pSortableColumn]="'isSeed'">
+ Seed
+ <p-sortIcon [field]="'isSeed'"></p-sortIcon>
+ </th>
+ <th>
+ Closest viral proteins
+ </th>
+ <th [pSortableColumn]="'closestDistance'">
+ Closest distance
+ <p-sortIcon [field]="'closestDistance'"></p-sortIcon>
+ </th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
@@ -305,7 +352,23 @@
</td>
<td><a href="https://www.uniprot.org/uniprot/{{ e.proteinAc }}" target="_blank">{{ e.proteinAc }}</a></td>
<td>{{e.name}}</td>
+ <td>{{e.proteinName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
+ <td>
+ <span *ngIf="e.isSeed">
+ <i class="fa fa-check"></i>
+ Seed
+ </span>
+ <span *ngIf="!e.isSeed">
+ <i class="fa fa-times"></i>
+ </span>
+ </td>
+ <td title="{{previewStringArray(e.closestViralProteins, 100)}}">
+ {{previewStringArray(e.closestViralProteins, 3)}}
+ </td>
+ <td>
+ {{e.closestDistance}}
+ </td>
</tr>
</ng-template>
</p-table>
@@ -340,6 +403,10 @@
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
+ <th [pSortableColumn]="'isSeed'">
+ Seed
+ <p-sortIcon [field]="'isSeed'"></p-sortIcon>
+ </th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
@@ -350,6 +417,15 @@
<td>{{e.effectName}}</td>
<td>{{e.virusName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
+ <td>
+ <span *ngIf="e.isSeed">
+ <i class="fa fa-asterisk has-text-primary"></i>
+ Seed
+ </span>
+ <span *ngIf="!e.isSeed">
+ <i class="fa fa-times"></i>
+ </span>
+ </td>
</tr>
</ng-template>
</p-table>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index c50a8e8a02a6b66ef55846d652cd4febac90d078..aea6445261e2252511dcdf795b4d77be86b12931 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -38,6 +38,15 @@ interface Scored {
rawScore: number; // Unnormalized (kept to restore unnormalized value)
}
+interface Seeded {
+ isSeed: boolean;
+}
+
+interface Baited {
+ closestViralProteins: string[];
+ closestDistance: number;
+}
+
@Component({
selector: 'app-analysis-panel',
templateUrl: './analysis-panel.component.html',
@@ -66,11 +75,11 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
private proteins: any;
public effects: any;
- public tableDrugs: Array<Drug & Scored> = [];
- public tableProteins: Array<Protein & Scored> = [];
- public tableSelectedProteins: Array<Protein & Scored> = [];
- public tableViralProteins: Array<ViralProtein & Scored> = [];
- public tableSelectedViralProteins: Array<ViralProtein & Scored> = [];
+ public tableDrugs: Array<Drug & Scored & Baited> = [];
+ public tableProteins: Array<Protein & Scored & Seeded & Baited> = [];
+ public tableSelectedProteins: Array<Protein & Scored & Seeded & Baited> = [];
+ public tableViralProteins: Array<ViralProtein & Scored & Seeded> = [];
+ public tableSelectedViralProteins: Array<ViralProtein & Scored & Seeded> = [];
public tableNormalize = false;
public tableHasScores = false;
@@ -89,9 +98,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
private async refresh() {
if (this.token) {
this.task = await this.getTask(this.token);
+ this.analysis.switchSelection(this.token);
if (this.task && this.task.info.done) {
const result = await this.http.get<any>(`${environment.backend}task_result/?token=${this.token}`).toPromise();
+ const nodeAttributes = result.nodeAttributes || {};
+ const isSeed: {[key: string]: boolean} = nodeAttributes.isSeed || {};
// Reset
this.nodeData = {nodes: null, edges: null};
@@ -112,12 +124,22 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.network = new vis.Network(container, this.nodeData, options);
const promises: Promise<any>[] = [];
+ promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=drugs`).toPromise()
+ .then((table) => {
+ this.tableDrugs = table;
+ this.tableDrugs.forEach((r) => {
+ r.rawScore = r.score;
+ r.closestViralProteins = (r.closestViralProteins as any).split(',');
+ });
+ }));
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=proteins`).toPromise()
.then((table) => {
this.tableProteins = table;
this.tableSelectedProteins = [];
this.tableProteins.forEach((r) => {
r.rawScore = r.score;
+ r.isSeed = isSeed[r.proteinAc];
+ r.closestViralProteins = (r.closestViralProteins as any).split(',');
if (this.analysis.proteinInSelection(r)) {
this.tableSelectedProteins.push(r);
}
@@ -126,12 +148,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=viral_proteins`).toPromise()
.then((table) => {
this.tableViralProteins = table;
- this.tableViralProteins.forEach((r) => r.rawScore = r.score);
- }));
- promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=drugs`).toPromise()
- .then((table) => {
- this.tableDrugs = table;
- this.tableDrugs.forEach((r) => r.rawScore = r.score);
+ this.tableViralProteins.forEach((r) => {
+ r.rawScore = r.score;
+ r.isSeed = isSeed[r.effectId];
+ });
}));
await Promise.all(promises);
@@ -221,10 +241,8 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
const nodeSelected = this.analysis.idInSelection(node.id);
- if (selected !== nodeSelected) {
- Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, node.isSeed, selected));
- updatedNodes.push(node);
- }
+ Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, node.isSeed, nodeSelected));
+ updatedNodes.push(node);
});
this.nodeData.nodes.update(updatedNodes);
@@ -266,6 +284,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
close() {
+ this.analysis.switchSelection('main');
this.token = null;
this.tokenChange.emit(this.token);
this.emitVisibleItems(false);
@@ -541,4 +560,13 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.analysis.removeItems(removeItems);
}
+ public previewStringArray(arr: string[], count: number): string {
+ if (arr.length < count) {
+ return arr.join(', ');
+ } else {
+ return arr.slice(0, count).join(', ') + `, ... (${arr.length})`;
+ }
+ }
}
+
+
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 743e71785ba6f4e38881bd264331dee29ea6b419..bc3986c80da16cfa86dee0e9f7899b93636c8a3d 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -11,6 +11,10 @@
{{ wrapper.data.proteinAc }}
</a>
</p>
+ <p>
+ <b><span>Name: </span></b>
+ {{ wrapper.data.proteinName }}
+ </p>
</div>
<div *ngIf="wrapper.type === 'virus'">
<p>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index e9a0ed4f002fb4102648d94d3deb78bd15adc5b7..3096d581541ddd4bf3503d941d7d5e0f99732937 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -82,7 +82,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
- All nodes with degree greater than this value times number of vertices will be ignored.
+ All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
@@ -162,7 +162,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
- All nodes with degree greater than this value times number of vertices will be ignored.
+ All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
@@ -229,7 +229,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
- All nodes with degree greater than this value times number of vertices will be ignored.
+ All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
@@ -273,18 +273,27 @@
</div>
<div class="field">
- <label class="label" for="keypathwayminer-k">K</label>
+ <label class="label" for="keypathwayminer-k">Additional proteins</label>
<div class="control">
<div class="select">
<select id="keypathwayminer-k" [(ngModel)]="keypathwayminerK">
<option [ngValue]="1">1</option>
<option [ngValue]="2">2</option>
<option [ngValue]="3">3</option>
- <option [ngValue]="4">4</option>
<option [ngValue]="5">5</option>
+ <option [ngValue]="10">10</option>
+ <option [ngValue]="15">15</option>
+ <option [ngValue]="20">20</option>
+ <option [ngValue]="25">25</option>
+ <option [ngValue]="30">30</option>
+ <option [ngValue]="40">40</option>
+ <option [ngValue]="50">50</option>
</select>
</div>
</div>
+ <p class="help">
+ Number of new proteins to be found.
+ </p>
</div>
<div class="box">
@@ -352,7 +361,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
- All nodes with degree greater than this value times number of vertices will be ignored.
+ All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 3dfb9de948b6f1da77f7c40d39ab6a60e494e2e8..83e9c35c1169d5c82e95fa56cec19272b7e5fb57 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -9,6 +9,7 @@ import {
QuickAlgorithmType,
TRUSTRANK
} from '../../analysis.service';
+import {Dataset} from '../../interfaces';
@Component({
selector: 'app-launch-analysis',
@@ -22,7 +23,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
@Input()
public target: 'drug' | 'drug-target';
@Input()
- public dataset;
+ public dataset: Dataset;
@Output()
public showChange = new EventEmitter<boolean>();
@@ -35,7 +36,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public trustrankIncludeNonApprovedDrugs = false;
public trustrankIncludeViralNonSeeds = true;
public trustrankDampingFactor = 0.85;
- public trustrankMaxDeg = 1.0;
+ public trustrankMaxDeg = 0;
public trustrankHubPenalty = 0.0;
public trustrankResultSize = 20;
@@ -43,24 +44,24 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public closenessIncludeIndirectDrugs = false;
public closenessIncludeNonApprovedDrugs = false;
public closenessIncludeViralNonSeeds = true;
- public closenessMaxDeg = 1.0;
+ public closenessMaxDeg = 0;
public closenessHubPenalty = 0.0;
public closenessResultSize = 20;
// Degree Parameters
public degreeIncludeNonApprovedDrugs = false;
public degreeIncludeViralNonSeeds = true;
- public degreeMaxDeg = 1.0;
+ public degreeMaxDeg = 0;
public degreeResultSize = 20;
// Keypathwayminer Parameters
- public keypathwayminerK = 1;
+ public keypathwayminerK = 5;
// Multisteiner Parameters
public multisteinerNumTrees = 5;
public multisteinerTolerance = 10;
public multisteinerIncludeViralNonSeeds = true;
- public multisteinerMaxDeg = 1.0;
+ public multisteinerMaxDeg = 0;
public multisteinerHubPenalty = 0.0;
public hasBaits;
@@ -97,37 +98,44 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
seeds: this.analysis.getSelection().map((item) => item.backendId),
};
+ parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset.backendId;
+ parameters.bait_datasets = this.dataset.data;
+
if (this.algorithm === 'trustrank') {
- parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.damping_factor = this.trustrankDampingFactor;
parameters.include_indirect_drugs = this.trustrankIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.trustrankIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.trustrankIncludeViralNonSeeds;
- parameters.max_deg = this.trustrankMaxDeg;
+ if (this.trustrankMaxDeg && this.trustrankMaxDeg > 0) {
+ parameters.max_deg = this.trustrankMaxDeg;
+ }
parameters.hub_penalty = this.trustrankHubPenalty;
parameters.result_size = this.trustrankResultSize;
} else if (this.algorithm === 'closeness') {
- parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.closenessIncludeViralNonSeeds;
- parameters.max_deg = this.closenessMaxDeg;
+ if (this.closenessMaxDeg && this.closenessMaxDeg > 0) {
+ parameters.max_deg = this.closenessMaxDeg;
+ }
parameters.hub_penalty = this.closenessHubPenalty;
parameters.result_size = this.closenessResultSize;
} else if (this.algorithm === 'degree') {
- parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_non_approved_drugs = this.degreeIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.degreeIncludeViralNonSeeds;
- parameters.max_deg = this.degreeMaxDeg;
+ if (this.degreeMaxDeg && this.degreeMaxDeg > 0) {
+ parameters.max_deg = this.degreeMaxDeg;
+ }
parameters.result_size = this.degreeResultSize;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
} else if (this.algorithm === 'multisteiner') {
- parameters.strain_or_drugs = this.dataset;
parameters.num_trees = this.multisteinerNumTrees;
parameters.tolerance = this.multisteinerTolerance;
parameters.ignore_non_seed_baits = !this.multisteinerIncludeViralNonSeeds;
- parameters.max_deg = this.multisteinerMaxDeg;
+ if (this.multisteinerMaxDeg && this.multisteinerMaxDeg > 0) {
+ parameters.max_deg = this.multisteinerMaxDeg;
+ }
parameters.hub_penalty = this.multisteinerHubPenalty;
}
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index f2448d717b1e03279199f3f5c8c7ce05b694603d..77e8b841f76b87f7955008e34ca5850cd866e18b 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -1,10 +1,9 @@
import {AlgorithmType, QuickAlgorithmType} from './analysis.service';
-export type NodeType = 'host' | 'virus' | 'drug';
-
export interface Protein {
name: string;
proteinAc: string;
+ proteinName: string;
effects?: ViralProtein[];
x?: number;
y?: number;
@@ -132,22 +131,10 @@ export function getWrapperFromDrug(drug: Drug): Wrapper {
export type WrapperType = 'host' | 'virus' | 'drug';
-export function getTypeFromNodeId(nodeId: string): WrapperType {
- if (nodeId.startsWith('p_')) {
- return 'host';
- }
- if (nodeId.startsWith('v_')) {
- return 'virus';
- }
- if (nodeId.startsWith('d_')) {
- return 'drug';
- }
-}
-
export interface Wrapper {
backendId: string;
nodeId: string;
- type: 'host' | 'virus' | 'drug';
+ type: WrapperType;
data: any;
}
@@ -156,6 +143,7 @@ export interface Drug {
name: string;
status: 'approved' | 'investigational';
inTrial: boolean;
+ inLiterature: boolean;
}
export interface Dataset {
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index be655e2aa1b2ce1c366b286d4fc6fa75d448c7d9..83d9bae024020c1993275743f7a8835bf0ace660 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -1,7 +1,7 @@
<div class="is-hidden-mobile">
<app-launch-analysis [(show)]="showAnalysisDialog"
[target]="analysisDialogTarget"
- [dataset]="selectedDataset.backendId">
+ [dataset]="selectedDataset">
</app-launch-analysis>
<app-custom-proteins [(show)]="showCustomProteinsDialog" [visibleNodes]="currentViewNodes">
@@ -133,7 +133,7 @@
<footer class="card-footer">
<a (click)="reset($event);" class="card-footer-item has-text-danger" data-tooltip="Remove filter and show all proteins.">
<span class="icon">
- <i class="fa fa-refresh"></i>
+ <i class="fa fa-broom"></i>
</span>
<span>
Reset
@@ -313,12 +313,12 @@
class="button is-primary is-fullwidth is-rounded has-tooltip"
data-tooltip="Find drug targets for the selected proteins."
[disabled]="analysis.getCount() === 0">
- <span class="icon">
- <i class="fa fa-crosshairs"></i>
- </span>
+ <span class="icon">
+ <i class="fa fa-crosshairs"></i>
+ </span>
<span>
- Find Drug Targets
- </span>
+ Find Drug Targets
+ </span>
</button>
</div>
</div>
@@ -328,15 +328,39 @@
class="button is-primary is-fullwidth is-rounded has-tooltip"
data-tooltip="Find drugs for the selected proteins."
[disabled]="analysis.getCount() === 0">
- <span class="icon">
- <i class="fa fa-capsules"></i>
- </span>
+ <span class="icon">
+ <i class="fa fa-capsules"></i>
+ </span>
<span>
- Find Drugs
- </span>
+ Find Drugs
+ </span>
</button>
</div>
</div>
+ <div class="field">
+ <div class="control">
+ <a *ngIf="analysis.getCount() > 0" [href]="gProfilerLink()" target="_blank"
+ class="button is-primary is-fullwidth is-rounded has-tooltip"
+ data-tooltip="Use enrichment analysis via g:Profiler (external).">
+ <span class="icon">
+ <i class="fa fa-external-link-alt"></i>
+ </span>
+ <span>
+ Enrichment Analysis
+ </span>
+ </a>
+ <a *ngIf="analysis.getCount() === 0" disabled
+ class="button is-primary is-fullwidth is-rounded has-tooltip"
+ data-tooltip="Use enrichment analysis via g:Profiler (external).">
+ <span class="icon">
+ <i class="fa fa-external-link-alt"></i>
+ </span>
+ <span>
+ Enrichment Analysis
+ </span>
+ </a>
+ </div>
+ </div>
</div>
</div>
</div>
@@ -368,7 +392,7 @@
<i class="fa fa-trash"></i>
</span>
<span>
- Delete All
+ Delete all
</span>
</a>
</footer>
@@ -423,34 +447,36 @@
Double-click on a protein to select it for the analysis.
</i>
</div>
+
<footer class="card-footer">
<a (click)="analysis.addVisibleHostProteins(currentViewNodes, currentViewProteins)"
class="card-footer-item has-text-success" data-tooltip="Add all visible host proteins.">
<span class="icon">
- <i class="fa fa-eye"></i>
+ <i class="fa fa-plus"></i>
</span>
<span>
- Host Proteins
+ Add host proteins
</span>
</a>
- <a (click)="analysis.addVisibleViralProteins(currentViewNodes, currentViewViralProteins)"
- class="card-footer-item has-text-success" data-tooltip="Add all visible viral proteins.">
+ <a (click)="analysis.removeAllHostProteins()"
+ class="card-footer-item has-text-danger" data-tooltip="Remove all host proteins.">
<span class="icon">
- <i class="fa fa-eye"></i>
+ <i class="fa fa-minus"></i>
</span>
<span>
- Viral Proteins
+ Remove host proteins
</span>
</a>
</footer>
+
<footer class="card-footer">
- <a (click)="analysis.removeAllHostProteins()"
- class="card-footer-item has-text-danger" data-tooltip="Remove all host proteins.">
+ <a (click)="analysis.addVisibleViralProteins(currentViewNodes, currentViewViralProteins)"
+ class="card-footer-item has-text-success" data-tooltip="Add all visible viral proteins.">
<span class="icon">
- <i class="fa fa-minus"></i>
+ <i class="fa fa-plus"></i>
</span>
<span>
- Host Proteins
+ Add viral proteins
</span>
</a>
<a (click)="analysis.removeAllViralProteins()"
@@ -459,10 +485,32 @@
<i class="fa fa-minus"></i>
</span>
<span>
- Viral Proteins
+ Remove viral proteins
</span>
</a>
</footer>
+
+ <footer class="card-footer" *ngIf="selectedAnalysisToken">
+ <a (click)="analysis.addSeeds(currentViewNodes)"
+ class="card-footer-item has-text-success" data-tooltip="Add all visible seeds.">
+ <span class="icon">
+ <i class="fa fa-plus"></i>
+ </span>
+ <span>
+ Add seeds
+ </span>
+ </a>
+ <a (click)="analysis.removeSeeds(currentViewNodes)"
+ class="card-footer-item has-text-danger" data-tooltip="Remove all seeds.">
+ <span class="icon">
+ <i class="fa fa-minus"></i>
+ </span>
+ <span>
+ Remove seeds
+ </span>
+ </a>
+ </footer>
+
<footer class="card-footer">
<a (click)="showCustomProteinsDialog = true" class="card-footer-item has-text-primary"
data-tooltip="Add a custom list of proteins.">
@@ -470,21 +518,32 @@
<i class="fa fa-upload"></i>
</span>
<span>
- Custom Proteins
+ Custom proteins
</span>
</a>
</footer>
+
<footer class="card-footer">
+ <a (click)="analysis.invertSelection(currentViewNodes)" class="card-footer-item has-text-primary"
+ data-tooltip="Invert the current selection.">
+ <span class="icon">
+ <i class="fa fa-sync"></i>
+ </span>
+ <span>
+ Invert
+ </span>
+ </a>
<a (click)="analysis.resetSelection()" class="card-footer-item has-text-danger"
- data-tooltip="Remove all entries of the selection.">
+ data-tooltip="Remove all entries from the selection.">
<span class="icon">
- <i class="fa fa-refresh"></i>
+ <i class="fa fa-broom"></i>
</span>
<span>
Reset
</span>
</a>
</footer>
+
</div>
</div>
</div>
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index a92060ae1ce055aef23be9a9885816401301723b..f76477839398fa60bfb5b2c4cfe1cea2bc928219 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -141,10 +141,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
const nodeSelected = this.analysis.idInSelection(node.id);
- if (selected !== nodeSelected) {
- Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, true, selected));
- updatedNodes.push(node);
- }
+ Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, true, nodeSelected));
+ updatedNodes.push(node);
});
this.nodeData.nodes.update(updatedNodes);
}
@@ -466,4 +464,26 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.currentViewViralProteins = this.effects;
}
}
+
+ gProfilerLink(): string {
+ const queryString = this.analysis.getSelection()
+ .filter(wrapper => wrapper.type === 'host')
+ .map(wrapper => wrapper.data.proteinAc)
+ .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=';
+ }
+
}
diff --git a/src/app/pages/home-page/home-page.component.html b/src/app/pages/home-page/home-page.component.html
index a9661338f8de01fbff22d1641942b7fb9d2359dc..32eadb29e2a2be65a8ce8aea81cd435925462b3b 100644
--- a/src/app/pages/home-page/home-page.component.html
+++ b/src/app/pages/home-page/home-page.component.html
@@ -3,7 +3,7 @@
<div class="container has-text-centered">
<div class="column">
<div class="logo-box is-hidden-mobile">
- <img src="assets/covex_logo.png" style="height: 200px; width: 600px">
+ <img src="assets/covex_logo.png" style="height: 233px; width: 600px">
</div>
<div class="has-text-centered video-box">
diff --git a/src/app/pages/home-page/home-page.component.scss b/src/app/pages/home-page/home-page.component.scss
index b3d5ed64d5fad618213b3ca0dd6ff6f571976d9a..27f2eb600561869c396767ac3809d433db1e1f39 100644
--- a/src/app/pages/home-page/home-page.component.scss
+++ b/src/app/pages/home-page/home-page.component.scss
@@ -1,6 +1,4 @@
img {
- width: 600px;
- height: 200px;
padding: 30px;
background-color: rgba(255, 255, 255, 0.7);
border-radius: 25px;
diff --git a/src/assets/covex_logo.jpg b/src/assets/covex_logo.jpg
deleted file mode 100644
index cb3c06274b7173d8752b4ea508a7c1a826b39de7..0000000000000000000000000000000000000000
Binary files a/src/assets/covex_logo.jpg and /dev/null differ
diff --git a/src/assets/covex_logo.png b/src/assets/covex_logo.png
index ff01400851865ccb47bec645a3cc22895377ffed..da0a57d1171e27eee1d8693d3ad6fa8eebd2068b 100644
Binary files a/src/assets/covex_logo.png and b/src/assets/covex_logo.png differ
diff --git a/src/assets/covex_logo_small.png b/src/assets/covex_logo_small.png
index d380da83d80039adc43e5d19b9ec06220b93e932..16bac8bbd786aabfaeeb69c05dd4d62b71ee3842 100644
Binary files a/src/assets/covex_logo_small.png and b/src/assets/covex_logo_small.png differ
diff --git a/src/styles.scss b/src/styles.scss
index 4ff262d2e2c44ec2f8ce2d8f50644825a27816a0..34a3572101b1c3c344ae95dbd90befdfc155473f 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -31,12 +31,9 @@ nav.navbar {
}
img.menu-icon.is-hoverable.navbar-item.logo {
- height: 45px;
+ height: 40px;
width: 125px;
- padding-top: 5px;
- padding-bottom: 10px;
- padding-left: 0px;
- padding-right: 0px;
+ padding: 0;
}
.landing {