From 5a40f9574b4644940dd9068a096fa8b44276d262 Mon Sep 17 00:00:00 2001
From: Julian Matschinske <ge93nar@mytum.de>
Date: Tue, 14 Apr 2020 13:36:42 +0200
Subject: [PATCH] Extend frontend with option to exclude viral non seed baits
---
.../analysis-window.component.html | 7 +++++
.../launch-analysis.component.html | 28 +++++++++++++++++++
.../launch-analysis.component.ts | 11 ++++++--
3 files changed, 44 insertions(+), 2 deletions(-)
diff --git a/src/app/components/analysis-window/analysis-window.component.html b/src/app/components/analysis-window/analysis-window.component.html
index c589a593..6c42eac0 100644
--- a/src/app/components/analysis-window/analysis-window.component.html
+++ b/src/app/components/analysis-window/analysis-window.component.html
@@ -59,6 +59,13 @@
<i *ngIf="!task.info.parameters.includeNonApprovedDrugs" class="fa fa-times"></i>
</td>
</tr>
+ <tr *ngIf="task.info.parameters.ignoreNonSeedBaits !== undefined && task.info.target === 'drug-target'">
+ <td>Include non-seed viral proteins</td>
+ <td>
+ <i *ngIf="!task.info.parameters.ignoreNonSeedBaits" class="fa fa-check"></i>
+ <i *ngIf="task.info.parameters.ignoreNonSeedBaits" class="fa fa-times"></i>
+ </td>
+ </tr>
<tr *ngIf="task.info.parameters.resultSize">
<td>Result Size</td>
<td>{{task.info.parameters.resultSize}}</td>
diff --git a/src/app/components/launch-analysis/launch-analysis.component.html b/src/app/components/launch-analysis/launch-analysis.component.html
index f4d81847..036a7041 100644
--- a/src/app/components/launch-analysis/launch-analysis.component.html
+++ b/src/app/components/launch-analysis/launch-analysis.component.html
@@ -70,6 +70,13 @@
required>
</div>
</div>
+ <div class="field" *ngIf="target === 'drug-target'">
+ <label class="label">Include non-seed viral proteins</label>
+ <app-toggle textOn="Include" textOff="Ignore"
+ tooltipOn="Include viral proteins that are not seeds."
+ tooltipOff="Exclude viral proteins that are not seeds."
+ [(value)]="trustrankIncludeViralNonSeeds"></app-toggle>
+ </div>
<div class="field">
<label class="label" for="trustrank-rs">Result Size</label>
<div class="control">
@@ -97,6 +104,13 @@
tooltipOff="Exclude non-approved drugs from the result."
[(value)]="closenessIncludeNonApprovedDrugs"></app-toggle>
</div>
+ <div class="field" *ngIf="target === 'drug-target'">
+ <label class="label">Include non-seed viral proteins</label>
+ <app-toggle textOn="Include" textOff="Ignore"
+ tooltipOn="Include viral proteins that are not seeds."
+ tooltipOff="Exclude viral proteins that are not seeds."
+ [(value)]="closenessIncludeViralNonSeeds"></app-toggle>
+ </div>
<div class="field">
<label class="label" for="closeness-rs">Result Size</label>
<div class="control">
@@ -118,6 +132,13 @@
tooltipOff="Exclude non-approved drugs from the result."
[(value)]="degreeIncludeNonApprovedDrugs"></app-toggle>
</div>
+ <div class="field" *ngIf="target === 'drug-target'">
+ <label class="label">Include non-seed viral proteins</label>
+ <app-toggle textOn="Include" textOff="Ignore"
+ tooltipOn="Include viral proteins that are not seeds."
+ tooltipOff="Exclude viral proteins that are not seeds."
+ [(value)]="degreeIncludeViralNonSeeds"></app-toggle>
+ </div>
<div class="field">
<label class="label" for="degree-rs">Result Size</label>
<div class="control">
@@ -190,6 +211,13 @@
</div>
</div>
</div>
+ <div class="field" *ngIf="target === 'drug-target'">
+ <label class="label">Include non-seed viral proteins</label>
+ <app-toggle textOn="Include" textOff="Ignore"
+ tooltipOn="Include viral proteins that are not seeds."
+ tooltipOff="Exclude viral proteins that are not seeds."
+ [(value)]="multisteinerIncludeViralNonSeeds"></app-toggle>
+ </div>
</div>
</section>
diff --git a/src/app/components/launch-analysis/launch-analysis.component.ts b/src/app/components/launch-analysis/launch-analysis.component.ts
index ed3aaace..c3575198 100644
--- a/src/app/components/launch-analysis/launch-analysis.component.ts
+++ b/src/app/components/launch-analysis/launch-analysis.component.ts
@@ -33,16 +33,19 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Trustrank Parameters
public trustrankIncludeIndirectDrugs = false;
public trustrankIncludeNonApprovedDrugs = false;
+ public trustrankIncludeViralNonSeeds = true;
public trustrankDampingFactor = 0.85;
public trustrankResultSize = 20;
// Closeness Parameters
public closenessIncludeIndirectDrugs = false;
public closenessIncludeNonApprovedDrugs = false;
+ public closenessIncludeViralNonSeeds = true;
public closenessResultSize = 20;
// Degree Parameters
public degreeIncludeNonApprovedDrugs = false;
+ public degreeIncludeViralNonSeeds = true;
public degreeResultSize = 20;
// Keypathwayminer Parameters
@@ -51,6 +54,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Multisteiner Parameters
public multisteinerNumTrees = 5;
public multisteinerTolerance = 10;
+ public multisteinerIncludeViralNonSeeds = true;
public hasBaits;
@@ -91,16 +95,18 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
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.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.result_size = this.closenessResultSize;
} else if (this.algorithm === 'degree') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
- parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
- parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
+ parameters.include_non_approved_drugs = this.degreeIncludeNonApprovedDrugs;
+ parameters.ignore_non_seed_baits = !this.degreeIncludeViralNonSeeds;
parameters.result_size = this.closenessResultSize;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
@@ -108,6 +114,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.strain_or_drugs = this.dataset;
parameters.num_trees = this.multisteinerNumTrees;
parameters.tolerance = this.multisteinerTolerance;
+ parameters.ignore_non_seed_baits = !this.multisteinerIncludeViralNonSeeds;
}
await this.analysis.startAnalysis(this.algorithm, this.target, parameters);
--
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