diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index a4a979d91cc79c5ef16818e95e8e147a1741e957..7d433bfbd9e5661cf4b83edf08aa5ea5498af11a 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -1,5 +1,5 @@
<div *ngIf="token">
- <div class="card analysis">
+ <div class="card analysis" [ngClass]="{'fullscreen': fullscreen}">
<header class="card-header">
<p class="card-header-title">
<span class="icon">
@@ -12,17 +12,50 @@
(click)="analysis.removeTask(token); close()"
class="card-header-icon"
aria-label="delete"
+ pTooltip="Delete analysis"
+ [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
+ tooltipPosition="left"
>
<span class="icon has-text-danger" title="Delete analysis">
<i class="fas fa-trash" aria-hidden="true"></i>
</span>
</a>
- <a (click)="close()" class="card-header-icon" aria-label="close">
+ <a
+ (click)="close()"
+ class="card-header-icon"
+ aria-label="close"
+ pTooltip="Close analysis"
+ [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
+ tooltipPosition="left"
+ >
<span class="icon" title="Close analysis">
<i class="fas fa-times color-danger" aria-hidden="true"></i>
</span>
</a>
+
+ <a
+ pTooltip="Open in fullscreen"
+ [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
+ tooltipPosition="left"
+ *ngIf="!fullscreen"
+ (click)="toggleFullscreen()"
+ class="card-header-icon"
+ >
+ <span class="icon is-small">
+ <i class="fas fa-expand"></i>
+ </span>
+ </a>
+ <a
+ title="close fullscreen"
+ *ngIf="fullscreen"
+ (click)="toggleFullscreen()"
+ class="card-header-icon"
+ >
+ <span class="icon is-small">
+ <i class="fas fa-compress"></i>
+ </span>
+ </a>
</header>
<div
class="card-content tab-header-small"
@@ -49,13 +82,17 @@
<div *ngIf="task">
<div class="columns m-1">
<div class="column content">
- <h4
- class="is-4 has-text-weight-bold"
- >
- <span class="icon">
- <i class="fas fa-wrench" aria-hidden="true"></i>
- </span>
- {{(['quick', 'super', 'connect', 'connectSelected'].indexOf(task.info.algorithm) === -1) ? 'Algorithm:' : 'Method:' }}
+ <h4 class="is-4 has-text-weight-bold">
+ <span class="icon">
+ <i class="fas fa-wrench" aria-hidden="true"></i>
+ </span>
+ {{
+ ["quick", "super", "connect", "connectSelected"].indexOf(
+ task.info.algorithm
+ ) === -1
+ ? "Algorithm:"
+ : "Method:"
+ }}
{{ algorithmNames[task.info.algorithm] }}
</h4>
</div>
@@ -64,156 +101,177 @@
<div class="column">
<table class="table is-narrow">
<tbody>
- <tr
- *ngIf="
+ <tr
+ *ngIf="
result && result.geneInteractionDataset !== undefined
"
- >
- <td>Protein-Protein Interaction Dataset</td>
- <td>
- {{ result.geneInteractionDataset.name }} (Version
- {{ result.geneInteractionDataset.version }})
- </td>
- </tr>
- <tr
- *ngIf="
+ >
+ <td>Protein-Protein Interaction Dataset</td>
+ <td>
+ {{ result.geneInteractionDataset.name }} (Version
+ {{ result.geneInteractionDataset.version }})
+ </td>
+ </tr>
+ <tr
+ *ngIf="
result && result.drugInteractionDataset !== undefined
"
- >
- <td>Protein-Drug Interaction Dataset</td>
- <td>
- {{ result.drugInteractionDataset.name }} (Version
- {{ result.drugInteractionDataset.version }})
- </td>
- </tr>
- <tr *ngIf="task.info.parameters.resultSize !== undefined">
- <td>Result Size</td>
- <td>{{ task.info.parameters.resultSize }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.k !== undefined">
- <td>K</td>
- <td>{{ task.info.parameters.k }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.numTrees !== undefined">
- <td>Number of trees</td>
- <td>{{ task.info.parameters.numTrees }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.tolerance !== undefined">
- <td>Tolerance</td>
- <td>{{ task.info.parameters.tolerance }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.dampingFactor !== undefined">
- <td>Damping Factor</td>
- <td>{{ task.info.parameters.dampingFactor }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.maxDeg !== undefined">
- <td>Maximum Degree</td>
- <td>{{ task.info.parameters.maxDeg }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.hubPenalty !== undefined">
- <td>Hub Penality</td>
- <td>{{ task.info.parameters.hubPenalty }}</td>
- </tr>
- <tr
- *ngIf="
+ >
+ <td>Protein-Drug Interaction Dataset</td>
+ <td>
+ {{ result.drugInteractionDataset.name }} (Version
+ {{ result.drugInteractionDataset.version }})
+ </td>
+ </tr>
+ <tr *ngIf="task.info.parameters.resultSize !== undefined">
+ <td>Result Size</td>
+ <td>{{ task.info.parameters.resultSize }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.k !== undefined">
+ <td>K</td>
+ <td>{{ task.info.parameters.k }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.numTrees !== undefined">
+ <td>Number of trees</td>
+ <td>{{ task.info.parameters.numTrees }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.tolerance !== undefined">
+ <td>Tolerance</td>
+ <td>{{ task.info.parameters.tolerance }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.dampingFactor !== undefined">
+ <td>Damping Factor</td>
+ <td>{{ task.info.parameters.dampingFactor }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.maxDeg !== undefined">
+ <td>Maximum Degree</td>
+ <td>{{ task.info.parameters.maxDeg }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.hubPenalty !== undefined">
+ <td>Hub Penality</td>
+ <td>{{ task.info.parameters.hubPenalty }}</td>
+ </tr>
+ <tr
+ *ngIf="
task.info.parameters.includeIndirectDrugs !== undefined &&
task.info.target === 'drug'
"
- >
- <td>Include indirect drugs</td>
- <td>
- <i
- *ngIf="task.info.parameters.includeIndirectDrugs"
- class="fa fa-check"
- ></i>
- <i
- *ngIf="!task.info.parameters.includeIndirectDrugs"
- class="fa fa-times color-danger"
- ></i>
- </td>
- </tr>
- <tr
- *ngIf="
+ >
+ <td>Include indirect drugs</td>
+ <td>
+ <i
+ *ngIf="task.info.parameters.includeIndirectDrugs"
+ class="fa fa-check"
+ ></i>
+ <i
+ *ngIf="!task.info.parameters.includeIndirectDrugs"
+ class="fa fa-times color-danger"
+ ></i>
+ </td>
+ </tr>
+ <tr
+ *ngIf="
task.info.parameters.includeNonApprovedDrugs !==
undefined && task.info.target === 'drug'
"
- >
- <td>Include non-approved drugs</td>
- <td>
- <i
- *ngIf="task.info.parameters.includeNonApprovedDrugs"
- class="fa fa-check"
- ></i>
- <i
- *ngIf="!task.info.parameters.includeNonApprovedDrugs"
- class="fa fa-times color-danger"
- ></i>
- </td>
- </tr>
+ >
+ <td>Include non-approved drugs</td>
+ <td>
+ <i
+ *ngIf="task.info.parameters.includeNonApprovedDrugs"
+ class="fa fa-check"
+ ></i>
+ <i
+ *ngIf="!task.info.parameters.includeNonApprovedDrugs"
+ class="fa fa-times color-danger"
+ ></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>
</div>
- <div class="columns m-1"
- *ngIf="['quick','super','connect','connectSelected'].indexOf(task.info.algorithm) > -1"
+ <div
+ class="columns m-1"
+ *ngIf="
+ ['quick', 'super', 'connect', 'connectSelected'].indexOf(
+ task.info.algorithm
+ ) > -1
+ "
>
<div class="column">
<h4 class="is-4 has-text-weight-bold">
- <span class="icon">
- <i class="fas fa-wrench" aria-hidden="true"></i>
- </span>
+ <span class="icon">
+ <i class="fas fa-wrench" aria-hidden="true"></i>
+ </span>
Algorithm:
{{ algorithmNames["multisteiner"] }}
</h4>
<table class="table is-narrow">
<tbody>
- <tr>
- <td>Number of Trees</td>
- <td>1</td>
- </tr>
- <tr>
- <td>Tolerance</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Hub Penality</td>
- <td>1</td>
- </tr>
+ <tr>
+ <td>Number of Trees</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>Tolerance</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>Hub Penality</td>
+ <td>1</td>
+ </tr>
</tbody>
</table>
</div>
</div>
- <div class="columns m-1" *ngIf="['quick','super'].indexOf(task.info.algorithm) > -1">
+ <div
+ class="columns m-1"
+ *ngIf="['quick', 'super'].indexOf(task.info.algorithm) > -1"
+ >
<div class="column">
<h4 class="is-4 has-text-weight-bold">
- <span class="icon">
- <i class="fas fa-wrench" aria-hidden="true"></i>
- </span>
+ <span class="icon">
+ <i class="fas fa-wrench" aria-hidden="true"></i>
+ </span>
Algorithm:
{{ algorithmNames["closeness"] }}
</h4>
<table class="table is-narrow">
<tbody>
- <tr>
- <td>Include indirect drugs</td>
- <td>
- <i class="fa fa-times"></i>
- </td>
- </tr>
- <tr>
- <td>Include non-approved drugs</td>
- <td>
- <i class="fa fa-check"></i>
- </td>
- </tr>
- <tr>
- <td>Hub Penality</td>
- <td>1</td>
- </tr>
- <tr>
- <td>Result Size</td>
- <td>10</td>
- </tr>
+ <tr>
+ <td>Include indirect drugs</td>
+ <td>
+ <i class="fa fa-times"></i>
+ </td>
+ </tr>
+ <tr>
+ <td>Include non-approved drugs</td>
+ <td>
+ <i class="fa fa-check"></i>
+ </td>
+ </tr>
+ <tr>
+ <td>Hub Penality</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>Result Size</td>
+ <td>10</td>
+ </tr>
</tbody>
</table>
</div>
@@ -223,10 +281,7 @@
<div class="tab-content" [class.is-visible]="tab === 'network'">
<!-- network start -->
- <app-network
- networkType="analysis"
- [nodeData]="nodeData"
- ></app-network>
+ <app-network networkType="analysis" [nodeData]="nodeData"></app-network>
<!-- network end -->
</div>
<div
@@ -263,16 +318,16 @@
class="button is-rounded has-tooltip is-small"
pTooltip="Normalize the scores"
[tooltipStyleClass]="
- 'drgstn drgstn-tooltip drgstn-tooltip-top'
- "
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
tooltipPosition="top"
[class.is-primary]="tableNormalize"
(click)="toggleNormalization(true)"
[ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
>
- <span class="icon is-small">
- <i class="fa fa-ruler-vertical"></i>
- </span>
+ <span class="icon is-small">
+ <i class="fa fa-ruler-vertical"></i>
+ </span>
<span>Normalization On</span>
</button>
</p>
@@ -281,8 +336,8 @@
class="button is-rounded has-tooltip is-small"
pTooltip="Disable normalization of the scores."
[tooltipStyleClass]="
- 'drgstn drgstn-tooltip drgstn-tooltip-top'
- "
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
tooltipPosition="top"
[class.is-primary]="!tableNormalize"
(click)="toggleNormalization(false)"
@@ -339,16 +394,16 @@
class="button is-rounded has-tooltip is-small"
pTooltip="Normalize the scores"
[tooltipStyleClass]="
- 'drgstn drgstn-tooltip drgstn-tooltip-top'
- "
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
tooltipPosition="top"
[class.is-primary]="tableNormalize"
(click)="toggleNormalization(true)"
[ngClass]="{ 'text-small': drugstoneConfig.smallStyle }"
>
- <span class="icon is-small">
- <i class="fa fa-ruler-vertical"></i>
- </span>
+ <span class="icon is-small">
+ <i class="fa fa-ruler-vertical"></i>
+ </span>
<span>Normalization On</span>
</button>
</p>
@@ -357,8 +412,8 @@
class="button is-rounded has-tooltip is-small"
pTooltip="Disable normalization of the scores."
[tooltipStyleClass]="
- 'drgstn drgstn-tooltip drgstn-tooltip-top'
- "
+ 'drgstn drgstn-tooltip drgstn-tooltip-top'
+ "
tooltipPosition="top"
[class.is-primary]="!tableNormalize"
(click)="toggleNormalization(false)"
diff --git a/src/app/components/analysis-panel/analysis-panel.component.scss b/src/app/components/analysis-panel/analysis-panel.component.scss
index 92b3e1380674851115135894a532fd7e87761833..8794e59bc14356bf3723af66c9aa38c199be6133 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.scss
+++ b/src/app/components/analysis-panel/analysis-panel.component.scss
@@ -6,6 +6,15 @@
width: 100% !important;
}
+.fullscreen{
+ position: fixed !important;
+ height: 100vh !important;
+ width: 100vw !important;
+ top: 0 !important;
+ left: 0 !important;
+ z-index: $fullscreen-z;
+}
+
.tab-header-small {
padding: 0 !important;
}
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 1745bcbaa9cf5bd400ea6a2708456f1f1ddd2b93..23ff59ce9977cd3066f47a077c9d4113aec5be2c 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -80,6 +80,8 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public result: any = null;
public myConfig: IConfig = JSON.parse(JSON.stringify(defaultConfig));
+ public fullscreen = false;
+
public network: any;
public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
// private drugNodes: any[] = [];
@@ -505,4 +507,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.analysis.addItems(addItems);
this.analysis.removeItems(removeItems);
}
+
+ public toggleFullscreen() {
+ this.fullscreen = !this.fullscreen;
+ console.log('this.fullscreen', this.fullscreen)
+ }
}
diff --git a/src/app/components/network/network-legend/network-legend.component.html b/src/app/components/network/network-legend/network-legend.component.html
index 89ca0d45f68329b5b9b532bb8259ef90ad43a039..f1c1912d84206f342365e90e057d4dd56e062d53 100644
--- a/src/app/components/network/network-legend/network-legend.component.html
+++ b/src/app/components/network/network-legend/network-legend.component.html
@@ -73,6 +73,13 @@
...
</span>
</th>
+ <th *ngSwitchCase="'ellipse'">
+ <span
+ class="node ellipse"
+ [style.background-color]="nodeGroup.value.color.background"
+ >
+ </span>
+ </th>
<th *ngSwitchDefault>
<span
class="node {{ nodeGroup.value.shape }}"
diff --git a/src/app/components/task-list/task-list.component.scss b/src/app/components/task-list/task-list.component.scss
index ec5bceefa372b1f007e9ec671231569e201a1783..156944455feb7c65ed424cacf38260cd0af95c47 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 6a5b84be6641137c609c734be38bb923b4440248..23f8f306c06f1206adabf7d010ec1aa71aa55bfa 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: true},
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 e7e3a040c39b7fe4710576a143f989bee2404195..728696d6c0aed4dae6af2a0e942ca301f709b9be 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -27,7 +27,7 @@
<div
[class.is-active]="algorithm === algo.slug"
*ngFor="let algo of algorithms"
- class="is-fullwidth"
+ class="is-fullwidth algorithm-button"
>
<a (click)="algorithm = algo.slug" class="is-boxed is-medium">
{{ algo.name }}
@@ -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.scss b/src/app/dialogs/launch-analysis/launch-analysis.component.scss
index f6c5d8357a2a165de67d433986f253fca3dbecdd..c1aefe6b67d008f0669916eea5a1c155e7db2478 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.scss
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.scss
@@ -23,7 +23,3 @@
margin-top: 15px;
font-size: 11px;
}
-
-div.is-active {
- background-color: var(--drgstn-primary);
-}
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 273822d56a599c053baa142ec9968bcf603143a0..752cdf6ef2c3a31c590d983dba855b2d2af6592a 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -17,6 +17,9 @@ 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 +36,38 @@ 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 +75,12 @@ 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 +116,7 @@ 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 +139,7 @@ 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 +148,14 @@ 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 +163,14 @@ 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 +180,7 @@ 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/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 0687ed358f32a13b64b6f8af1436e057bf6a37ce..82cf955590889b0b59b24050ce07dca17326dabb 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -1,6 +1,5 @@
<div id="appWindow" (window:resize)="onResize($event)">
<div class="is-hidden-mobile fullheight" id="appContainer">
-
<app-license-agreement></app-license-agreement>
<app-launch-analysis
@@ -10,7 +9,6 @@
>
</app-launch-analysis>
-
<app-add-expressed-proteins
[(show)]="showThresholdDialog"
[selectedTissue]="networkHandler.activeNetwork.currentViewSelectedTissue"
@@ -190,9 +188,15 @@
</div>
</div>
- <app-quick-drug-target *ngIf="drugstoneConfig.config.showConnectGenes" (taskEvent)="emitTaskEvent($event)"></app-quick-drug-target>
+ <app-quick-drug-target
+ *ngIf="drugstoneConfig.config.showConnectGenes"
+ (taskEvent)="emitTaskEvent($event)"
+ ></app-quick-drug-target>
- <app-quick-drug *ngIf="drugstoneConfig.config.showSimpleAnalysis" (taskEvent)="emitTaskEvent($event)"></app-quick-drug>
+ <app-quick-drug
+ *ngIf="drugstoneConfig.config.showSimpleAnalysis"
+ (taskEvent)="emitTaskEvent($event)"
+ ></app-quick-drug>
<div
*ngIf="drugstoneConfig.config.showAdvAnalysis"
@@ -465,17 +469,18 @@
</i>
</div>
-
<footer class="card-footer">
- <!-- <a (click)="analysis.invertSelection(currentViewNodes)" class="card-footer-item text-primary"
- tooltipPosition="top" pTooltip="Invert the current selection.">
+ <a
+ (click)="analysis.invertSelection(networkHandler.activeNetwork.currentViewNodes)"
+ class="card-footer-item text-primary"
+ tooltipPosition="top"
+ pTooltip="Invert the current selection."
+ >
<span class="icon">
<i class="fa fa-sync"></i>
</span>
- <span>
- Invert
- </span>
- </a> -->
+ <span> Invert </span>
+ </a>
<a
*ngIf="analysis.getSelection().length"
(click)="analysis.resetSelection()"
@@ -510,10 +515,7 @@
></app-analysis-panel>
</div>
<!-- explorer network -->
- <app-network
- networkType="explorer"
- [nodeData]="nodeData"
- ></app-network>
+ <app-network networkType="explorer" [nodeData]="nodeData"></app-network>
</div>
<!-- End network block -->
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index f43a78c29d1298d881fa41f788397398912fc418..6a521affe27571a63a15086fdf7fab440842ad3b 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -466,7 +466,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
* @param key
* @param values
*/
- public setConfigNodeGroup(key: string, nodeGroups: { [key: string]: NodeGroup }) {
+ public setConfigNodeGroup(key: string, nodeGroups: { [key: string]: NodeGroup } | {}) {
// make sure that return-groups (seeds, drugs, found nodes) are set
const defaultNodeGroups = JSON.parse(JSON.stringify(defaultConfig.nodeGroups));
// user merge function to do deep merge
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index b8c3735130b2b8cfe022e05e9828e59752d7e58c..40ac700e1cb0bc2a6e4f31bb86d3ca5e7c282577 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -177,16 +177,20 @@ export class AnalysisService {
public invertSelection(nodes) {
const newSelection = [];
nodes.forEach((node: Node) => {
+ if (node.drugstoneType !== 'protein') {
+ // only consider proteins
+ return
+ }
const wrapper = getWrapperFromNode(node);
if (!this.inSelection(wrapper)) {
newSelection.push(wrapper);
}
});
- this.selectedItems.clear();
+ this.resetSelection()
for (const wrapper of newSelection) {
- this.selectedItems.set(wrapper.nodeId, wrapper);
+ this.selectedItems.set(wrapper.id, wrapper);
}
- this.selectListSubject.next({items: newSelection, selected: null});
+ this.selectListSubject.next({items: newSelection, selected: true});
}
resetSelection() {
@@ -249,6 +253,7 @@ 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 77d89d189a44887565c3f17d5a554c361f47fa8f..c1f77a357967d3d484f724238a6d7b7f00ff4157 100644
--- a/src/index.html
+++ b/src/index.html
@@ -92,9 +92,9 @@
<drugst-one id="netexp1"
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]}}}'
+ 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":"ellipse"},"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>
diff --git a/src/stylesheets/styles.scss b/src/stylesheets/styles.scss
index 1acb530f787a809aaf875a81357d6266d6272277..c0a751a175469a03d6f6a9bfcf765f6dd779ed29 100644
--- a/src/stylesheets/styles.scss
+++ b/src/stylesheets/styles.scss
@@ -255,3 +255,5 @@
padding: 0.5rem 1rem;
line-height: 24px;
}
+
+
diff --git a/src/stylesheets/theme-styles.scss b/src/stylesheets/theme-styles.scss
index 1da0834c14566bd20a41035ba75fc4c4e7a7e711..38a35385d64cd33a74b43279d056871df5eeb542 100644
--- a/src/stylesheets/theme-styles.scss
+++ b/src/stylesheets/theme-styles.scss
@@ -55,14 +55,14 @@
border-color: var(--drgstn-border) !important;
}
- .fa-spinner {
- color: var(--drgstn-secondary) !important;
- }
-
.tabs.is-toggle a:hover {
background-color: var(--drgstn-panel) !important;
}
+ .fa-spinner {
+ color: var(--drgstn-secondary) !important;
+ }
+
.tabs li a {
border-bottom: none;
}
@@ -178,7 +178,6 @@
color: var(--drgstn-text-secondary) !important;
}
-
.text-primary {
color: var(--drgstn-primary) !important;
}
@@ -263,12 +262,10 @@
}
}
-
.ng-select.ng-select-opened > .ng-select-container .ng-arrow {
border-bottom-color: var(--drgstn-text-primary) !important;
}
-
::-webkit-scrollbar {
width: 10px !important;
}
@@ -293,8 +290,18 @@
.toast-times {
color: var(--drgstn-text-secondary) !important;
}
+
+ .algorithm-button.is-active {
+ a {
+ background-color: var(--drgstn-primary) !important;
+ }
+ a:hover {
+ background-color: var(--drgstn-primary) !important;
+ }
+ }
}
+
// scrolllbar styles
network-expander {
--thumbBG: var(--drgstn-primary) !important;
diff --git a/src/stylesheets/variables.scss b/src/stylesheets/variables.scss
index 93a9ab0380f2d390beee98d9b7257b31995d6e11..6c28503c3cfdbd7329f335e66298a85fcb3130cb 100644
--- a/src/stylesheets/variables.scss
+++ b/src/stylesheets/variables.scss
@@ -50,7 +50,7 @@ $legend-triangle-height: 29px;
$legend-hexagon-font-size: 38px;
$legend-diamond-size: 25px;
$legend-scaling: 0.8;
-$legend-scaling-small: 0.6;
+$legend-scaling-small: 0.75;
$height: 100%;