From 81fd7f8abe7ed706fb92e4d2188118bd9ad1475b Mon Sep 17 00:00:00 2001
From: "Hartung, Michael" <michael.hartung@uni-hamburg.de>
Date: Fri, 30 Sep 2022 17:39:58 +0200
Subject: [PATCH] Custom edges in algortihms; proper formatting of arrow
messages in task list
---
.../analysis-panel.component.html | 13 ++
.../task-list/task-list.component.scss | 2 +-
src/app/config.ts | 2 +
.../launch-analysis.component.html | 120 +++++++++++++++++-
.../launch-analysis.component.ts | 25 ++--
src/app/services/analysis/analysis.service.ts | 1 +
src/index.html | 2 +-
7 files changed, 152 insertions(+), 13 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index a4a979d9..d19df5f5 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -150,6 +150,19 @@
></i>
</td>
</tr>
+ <tr *ngIf="task.info.parameters.customEdges !== undefined">
+ <td>Include all displayed edges</td>
+ <td>
+ <i
+ *ngIf="task.info.parameters.customEdges"
+ class="fa fa-check"
+ ></i>
+ <i
+ *ngIf="!task.info.parameters.customEdges"
+ class="fa fa-times color-danger"
+ ></i>
+ </td>
+ </tr>
</tbody>
</table>
</div>
diff --git a/src/app/components/task-list/task-list.component.scss b/src/app/components/task-list/task-list.component.scss
index ec5bceef..15694445 100644
--- a/src/app/components/task-list/task-list.component.scss
+++ b/src/app/components/task-list/task-list.component.scss
@@ -20,7 +20,7 @@
font-size: 10px;
max-width: 215px;
max-height: 30px;
- overflow: scroll;
+ overflow-y: scroll;
border: 1px solid var(--drgstn-border);
display: inline-block;
}
diff --git a/src/app/config.ts b/src/app/config.ts
index abee66b7..a0726e73 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -72,6 +72,7 @@ export interface IConfig {
nodeGroups: { [key: string]: NodeGroup };
edgeGroups: { [key: string]: EdgeGroup };
selfReferences: boolean;
+ customEdges: {default: boolean, selectable: boolean};
interactionDrugProtein: InteractionDrugProteinDB;
interactionProteinProtein: InteractionProteinProteinDB;
indicationDrugDisorder: IndicationDrugDisorderDB;
@@ -162,6 +163,7 @@ export const defaultConfig: IConfig = {
networkMenuButtonAnimationLabel: 'Animation',
identifier: 'symbol',
selfReferences: false,
+ customEdges: {default: true, selectable: false},
interactionDrugProtein: 'NeDRex',
interactionProteinProtein: 'NeDRex',
indicationDrugDisorder: 'NeDRex',
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index e7e3a040..e683e9bd 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -162,6 +162,25 @@
</div>
<p class="has-text-info is-size-7">Penalty parameter for hubs.</p>
</div>
+
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="trustrankCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
</div>
<div *ngIf="algorithm === 'closeness'">
@@ -261,6 +280,25 @@
</div>
<p class="has-text-info is-size-7">Penalty parameter for hubs.</p>
</div>
+
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="closenessCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
</div>
<div *ngIf="algorithm === 'degree'">
@@ -327,6 +365,25 @@
Disabled if equal to 0.
</p>
</div>
+
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="degreeCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
</div>
<div *ngIf="algorithm === 'proximity'">
@@ -407,6 +464,25 @@
</div>
<p class="has-text-info is-size-7">Penalty parameter for hubs.</p>
</div>
+
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="proximityCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
</div>
<div *ngIf="algorithm === 'betweenness'">
@@ -477,6 +553,25 @@
</div>
<p class="has-text-info is-size-7">Penalty parameter for hubs.</p>
</div>
+
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="betweennessCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
</div>
<div *ngIf="algorithm === 'keypathwayminer'">
@@ -537,8 +632,9 @@
<p>
The Multi-level Steiner Tree algorithm can be used to
approximate a minimum spanning subnetwork between seed
- nodes, which happen to be central interaction partners between the seed nodes, and thus represent
- favorable drug-targets (Ahmed et al. 2019).
+ nodes, which happen to be central interaction partners
+ between the seed nodes, and thus represent favorable
+ drug-targets (Ahmed et al. 2019).
</p>
</div>
</div>
@@ -627,8 +723,26 @@
</div>
<p class="has-text-info is-size-7">Penalty parameter for hubs.</p>
</div>
- </div>
+ <div
+ class="field"
+ *ngIf="drugstoneConfig.config.customEdges.selectable"
+ >
+ <label class="label">Include all displayed edges</label>
+ <app-toggle
+ textOn="Include"
+ textOff="Ignore"
+ tooltipOn="Use all edges from the visualized network and the Drugst.One database."
+ tooltipOff="Use only Drugst.One edges."
+ [(value)]="multisteinerCustomEdges"
+ >
+ </app-toggle>
+ <p class="has-text-info is-size-7">
+ Include PPI edges from displayed network in the algorithms or
+ use only edges from the Drugst.One database.
+ </p>
+ </div>
+ </div>
</div>
</div>
</section>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 273822d5..fbec89c9 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 {
import { Algorithm, AlgorithmType, QuickAlgorithmType } from 'src/app/interfaces';
import { DrugstoneConfigService } from 'src/app/services/drugstone-config/drugstone-config.service';
import {NetworkHandlerService} from "../../services/network-handler/network-handler.service";
+import { connectableObservableDescriptor } from 'rxjs/internal/observable/ConnectableObservable';
@Component({
selector: 'app-launch-analysis',
@@ -17,6 +18,9 @@ import {NetworkHandlerService} from "../../services/network-handler/network-hand
})
export class LaunchAnalysisComponent implements OnInit, OnChanges {
+ constructor(public analysis: AnalysisService, public drugstoneConfig: DrugstoneConfigService, public networkHandler: NetworkHandlerService) {
+ }
+
@Input()
public show = false;
@Input()
@@ -33,37 +37,38 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Trustrank Parameters
public trustrankIncludeIndirectDrugs = false;
public trustrankIncludeNonApprovedDrugs = false;
- public trustrankIncludeViralNonSeeds = true;
public trustrankDampingFactor = 0.85;
public trustrankMaxDeg = 0;
public trustrankHubPenalty = 0.0;
public trustrankResultSize = 20;
+ public trustrankCustomEdges = this.drugstoneConfig.config.customEdges.default;
// Closeness Parameters
public closenessIncludeIndirectDrugs = false;
public closenessIncludeNonApprovedDrugs = false;
- public closenessIncludeViralNonSeeds = true;
public closenessMaxDeg = 0;
public closenessHubPenalty = 0.0;
public closenessResultSize = 20;
+ public closenessCustomEdges = this.drugstoneConfig.config.customEdges.default;
// Degree Parameters
public degreeIncludeNonApprovedDrugs = false;
- public degreeIncludeViralNonSeeds = true;
public degreeMaxDeg = 0;
public degreeResultSize = 20;
+ public degreeCustomEdges = this.drugstoneConfig.config.customEdges.default;
// Network proximity
public proximityIncludeNonApprovedDrugs = false;
public proximityMaxDeg = 0;
public proximityHubPenalty = 0.0;
public proximityResultSize = 20;
+ public proximityCustomEdges = this.drugstoneConfig.config.customEdges.default;
// Betweenness Parameters
- public betweennessIncludeViralNonSeeds = true;
public betweennessMaxDeg = 0;
public betweennessHubPenalty = 0.0;
public betweennessResultSize = 20;
+ public betweennessCustomEdges = this.drugstoneConfig.config.customEdges.default;
// Keypathwayminer Parameters
public keypathwayminerK = 5;
@@ -71,15 +76,12 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Multisteiner Parameters
public multisteinerNumTrees = 5;
public multisteinerTolerance = 10;
- public multisteinerIncludeViralNonSeeds = true;
public multisteinerMaxDeg = 0;
public multisteinerHubPenalty = 0.0;
+ public multisteinerCustomEdges = this.drugstoneConfig.config.customEdges.default;
public maxTasks = MAX_TASKS;
- constructor(public analysis: AnalysisService, public drugstoneConfig: DrugstoneConfigService, public networkHandler: NetworkHandlerService) {
- }
-
ngOnInit(): void {
}
@@ -115,6 +117,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
config: this.drugstoneConfig.config,
input_network: this.networkHandler.activeNetwork.inputNetwork
};
+ console.log(parameters)
parameters.ppi_dataset = this.drugstoneConfig.config.interactionProteinProtein;
parameters.pdi_dataset = this.drugstoneConfig.config.interactionDrugProtein;
parameters.licenced = this.drugstoneConfig.config.licensedDatasets;
@@ -137,6 +140,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
parameters.hub_penalty = this.trustrankHubPenalty;
parameters.result_size = this.trustrankResultSize;
+ parameters.custom_edges = this.trustrankCustomEdges;
} else if (this.algorithm === 'closeness') {
parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
@@ -145,12 +149,14 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
parameters.hub_penalty = this.closenessHubPenalty;
parameters.result_size = this.closenessResultSize;
+ parameters.custom_edges = this.closenessCustomEdges;
} else if (this.algorithm === 'degree') {
parameters.include_non_approved_drugs = this.degreeIncludeNonApprovedDrugs;
if (this.degreeMaxDeg && this.degreeMaxDeg > 0) {
parameters.max_deg = this.degreeMaxDeg;
}
parameters.result_size = this.degreeResultSize;
+ parameters.custom_edges = this.degreeCustomEdges;
} else if (this.algorithm === 'proximity') {
parameters.include_non_approved_drugs = this.proximityIncludeNonApprovedDrugs;
if (this.proximityMaxDeg && this.proximityMaxDeg > 0) {
@@ -158,12 +164,14 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
parameters.hub_penalty = this.proximityHubPenalty;
parameters.result_size = this.proximityResultSize;
+ parameters.custom_edges = this.proximityCustomEdges;
} else if (this.algorithm === 'betweenness') {
if (this.betweennessMaxDeg && this.betweennessMaxDeg > 0) {
parameters.max_deg = this.betweennessMaxDeg;
}
parameters.hub_penalty = this.betweennessHubPenalty;
parameters.result_size = this.betweennessResultSize;
+ parameters.custom_edges = this.betweennessCustomEdges;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
} else if (this.algorithm === 'multisteiner') {
@@ -173,6 +181,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.max_deg = this.multisteinerMaxDeg;
}
parameters.hub_penalty = this.multisteinerHubPenalty;
+ parameters.custom_edges = this.multisteinerCustomEdges;
}
const token = await this.analysis.startAnalysis(this.algorithm, this.target, parameters);
const object = { taskId: token, algorithm: this.algorithm, target: this.target, params: parameters };
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index b8c37351..f39a5613 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -249,6 +249,7 @@ export class AnalysisService {
target: target,
num_trees: 5,
tolerance: 10,
+ custom_edges: this.drugstoneConfig.config.customEdges.default,
};
diff --git a/src/index.html b/src/index.html
index 77d89d18..63df1e94 100644
--- a/src/index.html
+++ b/src/index.html
@@ -94,7 +94,7 @@
pluginId="2"
groups='{"nodeGroups":{"patient":{"type":"patient","color":"#000000","font":{"color":"#000000"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"#000000","font":{"color":"#000000"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"#000000","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}}}'
config='{"expandNetworkMenu": false, "showSimpleAnalysis": true, "licensedDatasets": false, "physicsOn":false,"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":true,"showLegend":true}'
- network='{"nodes":[{"id": "FOXP3"},{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"BRCA1","to":"BRCA2","group":"ggi"},{"from":"ATM","to":"BARD1","group":"ggi"},{"from":"BRCA1","to":"CHEK2","group":"ggi"},{"from":"RAD51C","to":"RAD51D","group":"ggi"},{"from":"STK11","to":"TP53","group":"ggi"},{"from":"TP53","to":"PALB2","group":"ggi"},{"from":"TP53","to":"RAD51D","group":"ggi"},{"from":"TP53","to":"NF1","group":"ggi"},{"from":"TP53","to":"BRCA1","group":"ggi"},{"from":"TP53","to":"BRCA2","group":"ggi"},{"from":"PTEN","to":"BRCA1","group":"ggi"},{"from":"PTEN","to":"BRCA2","group":"ggi"},{"from":"TP53","to":"PTEN","group":"ggi"},{"from":"ATM","to":"PTEN","group":"ggi"},{"from":"CDH1","to":"RAD51D","group":"ggi"},{"from":"CDH1","to":"PALB2","group":"ggi"},{"from":"NBN","to":"BRIP1","group":"ggi"},{"from":"BRIP1","to":"PTEN","group":"ggi"},{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'
+ network='{"nodes":[{"id": "FOXP3"},{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"PTEN","to":"NBN","group":"ggi"}, {"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'
>
</drugst-one>
--
GitLab