diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 32e3a0e6c7cc40c8991fe0c299a1f54a4f3d2dfd..95d06d2480d06b16d76a4414063966b514fde05f 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -138,101 +138,104 @@
</div>
<footer *ngIf="myConfig.showFooter" class="card-footer toolbar network-footer-toolbar">
+
+ <div class="network-footer-toolbar-inner-container">
- <ng-container *ngIf="myConfig.showFooterButtonScreenshot">
- <button class="button is-primary is-rounded has-tooltip"
- pTooltip="Take a screenshot of the current network." tooltipPosition="top" (click)="toImage()">
- <span class="icon">
- <i class="fas fa-camera" aria-hidden="true"></i>
- </span>
- <span [ngClass]="{'text-normal':smallStyle}">
- Screenshot
- </span>
- </button>
- </ng-container>
+ <ng-container *ngIf="myConfig.showFooterButtonScreenshot">
+ <button class="button is-primary is-rounded has-tooltip network-footer-toolbar-element"
+ pTooltip="Take a screenshot of the current network." tooltipPosition="top" (click)="toImage()">
+ <span class="icon">
+ <i class="fas fa-camera" aria-hidden="true"></i>
+ </span>
+ <span [ngClass]="{'text-normal':smallStyle}">
+ Screenshot
+ </span>
+ </button>
+ </ng-container>
- <div class="field">
- <p class="control footer-buttons">
- <a [href]="graphmlLink()" class="button is-success is-rounded has-tooltip"
- pTooltip="Export this network as .graphml file." tooltipPosition="top">
- <span class="icon">
- <i class="fas fa-download" aria-hidden="true"></i>
- </span>
- <span [ngClass]="{'text-normal':smallStyle}">
- Export as .graphml
- </span>
- </a>
- </p>
- </div>
+ <div class="field network-footer-toolbar-element">
+ <p class="control footer-buttons">
+ <a [href]="graphmlLink()" class="button is-success is-rounded has-tooltip"
+ pTooltip="Export this network as .graphml file." tooltipPosition="top">
+ <span class="icon">
+ <i class="fas fa-download" aria-hidden="true"></i>
+ </span>
+ <span [ngClass]="{'text-normal':smallStyle}">
+ Export as .graphml
+ </span>
+ </a>
+ </p>
+ </div>
- <!-- <div class="field">-->
- <!-- <p class="control footer-buttons">-->
- <!-- <button class="button is-danger is-rounded has-tooltip" data-tooltip="Delete the current analysis."-->
- <!-- (click)="analysis.removeTask(token); close()">-->
- <!-- <span class="icon">-->
- <!-- <i class="fas fa-trash" aria-hidden="true"></i>-->
- <!-- </span>-->
- <!-- <span>-->
- <!-- Delete Analysis-->
- <!-- </span>-->
- <!-- </button>-->
- <!-- </p>-->
- <!-- </div>-->
+ <!-- <div class="field">-->
+ <!-- <p class="control footer-buttons">-->
+ <!-- <button class="button is-danger is-rounded has-tooltip" data-tooltip="Delete the current analysis."-->
+ <!-- (click)="analysis.removeTask(token); close()">-->
+ <!-- <span class="icon">-->
+ <!-- <i class="fas fa-trash" aria-hidden="true"></i>-->
+ <!-- </span>-->
+ <!-- <span>-->
+ <!-- Delete Analysis-->
+ <!-- </span>-->
+ <!-- </button>-->
+ <!-- </p>-->
+ <!-- </div>-->
- <div class="footer-buttons dropdown is-up" [class.is-active]="expressionExpanded">
- <div class="dropdown-trigger">
- <button (click)="expressionExpanded=!expressionExpanded"
- class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
- aria-haspopup="true" aria-controls="dropdown-menu" [ngClass]="{'button-small':smallStyle}"
- pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
- >
- <div [ngClass]="{'text-small':smallStyle}">
- <span *ngIf="!selectedTissue">Tissue</span>
- <span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
- <span class="icon is-small">
- <i class="fas"
- [class.fa-angle-up]="expressionExpanded"
- [class.fa-angle-left]="!expressionExpanded" aria-hidden="true"></i>
- </span>
- </div>
- </button>
- </div>
- <div class="dropdown-menu" id="dropdown-menu" role="menu">
- <div class="dropdown-content tissue-dropdown" [ngClass]="{'button-small':smallStyle}">
- <div class="scroll-area" [ngClass]="{'text-small':smallStyle}">
- <a (click)="selectTissue(null)"
- [class.is-active]="!selectedTissue"
- class="dropdown-item">
- None
- </a>
- <a *ngFor="let tissue of analysis.getTissues()"
- (click)="selectTissue(tissue)"
- [class.is-active]="selectedTissue && tissue.netexId === selectedTissue.netexId"
- class="dropdown-item">
- {{tissue.name}}
- </a>
+ <div class="footer-buttons dropdown is-up network-footer-toolbar-element" [class.is-active]="expressionExpanded">
+ <div class="dropdown-trigger">
+ <button (click)="expressionExpanded=!expressionExpanded"
+ class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
+ aria-haspopup="true" aria-controls="dropdown-menu" [ngClass]="{'button-small':smallStyle}"
+ pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
+ >
+ <div [ngClass]="{'text-small':smallStyle}">
+ <span *ngIf="!selectedTissue">Tissue</span>
+ <span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
+ <span class="icon is-small">
+ <i class="fas"
+ [class.fa-angle-up]="expressionExpanded"
+ [class.fa-angle-left]="!expressionExpanded" aria-hidden="true"></i>
+ </span>
+ </div>
+ </button>
+ </div>
+ <div class="dropdown-menu" id="dropdown-menu" role="menu">
+ <div class="dropdown-content tissue-dropdown" [ngClass]="{'button-small':smallStyle}">
+ <div class="scroll-area" [ngClass]="{'text-small':smallStyle}">
+ <a (click)="selectTissue(null)"
+ [class.is-active]="!selectedTissue"
+ class="dropdown-item">
+ None
+ </a>
+ <a *ngFor="let tissue of analysis.getTissues()"
+ (click)="selectTissue(tissue)"
+ [class.is-active]="selectedTissue && tissue.netexId === selectedTissue.netexId"
+ class="dropdown-item">
+ {{tissue.name}}
+ </a>
+ </div>
</div>
</div>
</div>
- </div>
- <app-toggle class="footer-buttons" textOn="Seeds On" textOff="Off"
- tooltipOn="Highlight seed nodes ON."
- tooltipOff="Highlight seed nodes OFF."
- [smallStyle]="smallStyle"
- [value]="highlightSeeds" (valueChange)="updateHighlightSeeds($event)"></app-toggle>
+ <app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Seeds On" textOff="Off"
+ tooltipOn="Highlight seed nodes ON."
+ tooltipOff="Highlight seed nodes OFF."
+ [smallStyle]="smallStyle"
+ [value]="highlightSeeds" (valueChange)="updateHighlightSeeds($event)"></app-toggle>
- <app-toggle *ngIf="task.info.target === 'drug-target'" class="footer-buttons" textOn="Drugs On" textOff="Off"
- tooltipOn="Display adjacent drugs ON."
- tooltipOff="Display adjacent drugs OFF."
- [smallStyle]="smallStyle"
- [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
+ <app-toggle *ngIf="task.info.target === 'drug-target'" class="footer-buttons network-footer-toolbar-element" textOn="Drugs On" textOff="Off"
+ tooltipOn="Display adjacent drugs ON."
+ tooltipOff="Display adjacent drugs OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
- <app-toggle class="footer-buttons" textOn="Animation On" textOff="Off"
- tooltipOn="Enable the network animation."
- tooltipOff="Disable the network animation and freeze nodes."
- [smallStyle]="smallStyle"
- [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
+ <app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Animation On" textOff="Off"
+ tooltipOn="Enable the network animation."
+ tooltipOff="Disable the network animation and freeze nodes."
+ [smallStyle]="smallStyle"
+ [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
+ </div>
</footer>
</div>
<div class="content tab-content scrollable table-tab" *ngIf="task && task.info.done" [class.is-visible]="tab === 'table'">
diff --git a/src/app/components/analysis-panel/analysis-panel.component.scss b/src/app/components/analysis-panel/analysis-panel.component.scss
index e4cf77d38f15b3acec6412ca1ea4bf0fedccabf1..34923202bc25922ab092d504c1c9c8dd6c435940 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.scss
+++ b/src/app/components/analysis-panel/analysis-panel.component.scss
@@ -73,3 +73,10 @@
overflow-y: auto;
}
+.network-footer-toolbar{
+ .dropdown-menu{
+ z-index: $analysis-network-toolbar-dropdown-z;
+ }
+}
+
+
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 1a7b525b74aa9c398d8bf86fe826e7e91d5ae871..9363902466fbcb707c58bec7e17a309540e8f333 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -115,6 +115,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public tableProteinScoreTooltip = '';
public expressionMap: NodeAttributeMap;
+ public gradientMap: NodeAttributeMap;
constructor(private http: HttpClient, public analysis: AnalysisService, public netex: NetexControllerService) {
}
@@ -267,12 +268,13 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
node.x = pos[item.id].x;
node.y = pos[item.id].y;
const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
+ const gradient = (this.gradientMap !== {}) && (this.gradientMap[item.id]) ? this.gradientMap[item.id] : 1.0;
const nodeStyled = NetworkSettings.getNodeStyle(
node,
this.myConfig,
isSeed,
selected,
- 1.0
+ gradient
)
updatedNodes.push(nodeStyled);
}
@@ -294,6 +296,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.tableSelectedProteins = [...proteinSelection];
this.tableSelectedViralProteins = [...viralProteinSelection];
} else {
+ // else: selected is null
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
let drugType;
@@ -302,12 +305,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
drugType = node.wrapper.data.status;
drugInTrial = node.wrapper.data.inTrial;
}
+ const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
+ const gradient = (this.gradientMap !== {}) && (this.gradientMap[node.id]) ? this.gradientMap[node.id] : 1.0;
const nodeStyled = NetworkSettings.getNodeStyle(
node,
this.myConfig,
- false,
+ isSeed,
selected,
- 1.0
+ gradient
)
updatedNodes.push(nodeStyled);
});
@@ -652,12 +657,13 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const pos = this.network.getPositions([item.id]);
node.x = pos[item.id].x;
node.y = pos[item.id].y;
+ const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
Object.assign(
node,
NetworkSettings.getNodeStyle(
node,
this.myConfig,
- false,
+ isSeed,
this.analysis.inSelection(getWrapperFromNode(item)),
1.0
)
@@ -667,6 +673,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.nodeData.nodes.update(updatedNodes);
// delete expression values
this.expressionMap = undefined;
+ this.gradientMap = {};
} else {
this.selectedTissue = tissue
const minExp = 0.3;
@@ -693,18 +700,19 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
continue;
}
const wrapper = getWrapperFromNode(node)
- const gradient = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
+ this.gradientMap[netexId] = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
const pos = this.network.getPositions([networkId]);
node.x = pos[networkId].x;
node.y = pos[networkId].y;
+ const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
Object.assign(node,
NetworkSettings.getNodeStyle(
node,
this.myConfig,
- false, // node.isSeed,
+ isSeed,
this.analysis.inSelection(wrapper),
- gradient));
- node.gradient = gradient;
+ this.gradientMap[netexId]));
+ node.gradient = this.gradientMap[netexId];
updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 2e6a5760d437d7ee8a0800498ebbb1b65bcb2ac0..cab05e038dc8882bcd5d47fb10bb085379c7721c 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -35,7 +35,7 @@ export type legendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget'
'drugTargetAndSeeds' | 'drugAndSeeds';
/// netexId to expressionlvl
-export type NodeAttributeMap = { string: number };
+export type NodeAttributeMap = { string: number } | {};
export interface NodeInteraction {
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 9cc38a205907ad93fa79fceeb019f7398b2efa86..2cf67c4595d470b67f76723c0252567bef7f773b 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -132,67 +132,69 @@
<footer *ngIf="myConfig.showFooter" class="card-footer toolbar network-footer-toolbar">
- <ng-container *ngIf="myConfig.showFooterButtonScreenshot">
- <button (click)="toImage()" class="button is-primary is-rounded has-tooltip network-footer-toolbar-element"
- pTooltip="Take a screenshot of the current network." tooltipPosition="top">
- <span class="icon">
- <i class="fas fa-camera" aria-hidden="true"></i>
- </span>
- <span [ngClass]="{'text-normal':smallStyle}">Screenshot</span>
- </button>
- </ng-container>
-
- <ng-container *ngIf="myConfig.showFooterButtonExpression">
- <div class="footer-buttons dropdown is-up network-footer-toolbar-element" [class.is-active]="expressionExpanded">
-
- <div class="dropdown-trigger">
- <button (click)="expressionExpanded=!expressionExpanded"
- class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
- aria-haspopup="true" aria-controls="dropdown-menu"
- pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
- [ngClass]="{'button-small':smallStyle}">
- <span *ngIf="!selectedTissue" [ngClass]="{'text-small':smallStyle}">Tissue</span>
- <span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
- <span *ngIf="expressionExpanded" class="icon is-small">
- <i class="fas fa-angle-up" aria-hidden="true"></i>
- </span>
- <span *ngIf="!expressionExpanded" class="icon is-small">
- <i class="fas fa-angle-left" aria-hidden="true"></i>
- </span>
- </button>
- </div>
- <div class="dropdown-menu" id="dropdown-menu" role="menu">
- <div class="dropdown-content tissue-dropdown">
- <div class="scroll-area">
- <a (click)="selectTissue(null)"
- [class.is-active]="!selectedTissue"
- class="dropdown-item">
- None
- </a>
- <a *ngFor="let tissue of analysis.getTissues()"
- (click)="selectTissue(tissue)"
- [class.is-active]="selectedTissue && tissue.netexId === selectedTissue.netexId"
- class="dropdown-item">
- {{tissue.name}}
- </a>
+ <div class="network-footer-toolbar-inner-container">
+
+ <ng-container *ngIf="myConfig.showFooterButtonScreenshot">
+ <button (click)="toImage()" class="button is-primary is-rounded has-tooltip network-footer-toolbar-element"
+ pTooltip="Take a screenshot of the current network." tooltipPosition="top">
+ <span class="icon">
+ <i class="fas fa-camera" aria-hidden="true"></i>
+ </span>
+ <span [ngClass]="{'text-normal':smallStyle}">Screenshot</span>
+ </button>
+ </ng-container>
+
+ <ng-container *ngIf="myConfig.showFooterButtonExpression">
+ <div class="footer-buttons dropdown is-up network-footer-toolbar-element" [class.is-active]="expressionExpanded">
+
+ <div class="dropdown-trigger">
+ <button (click)="expressionExpanded=!expressionExpanded"
+ class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
+ aria-haspopup="true" aria-controls="dropdown-menu"
+ pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
+ [ngClass]="{'button-small':smallStyle}">
+ <span *ngIf="!selectedTissue" [ngClass]="{'text-small':smallStyle}">Tissue</span>
+ <span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
+ <span *ngIf="expressionExpanded" class="icon is-small">
+ <i class="fas fa-angle-up" aria-hidden="true"></i>
+ </span>
+ <span *ngIf="!expressionExpanded" class="icon is-small">
+ <i class="fas fa-angle-left" aria-hidden="true"></i>
+ </span>
+ </button>
+ </div>
+ <div class="dropdown-menu" id="dropdown-menu" role="menu">
+ <div class="dropdown-content tissue-dropdown">
+ <div class="scroll-area">
+ <a (click)="selectTissue(null)"
+ [class.is-active]="!selectedTissue"
+ class="dropdown-item">
+ None
+ </a>
+ <a *ngFor="let tissue of analysis.getTissues()"
+ (click)="selectTissue(tissue)"
+ [class.is-active]="selectedTissue && tissue.netexId === selectedTissue.netexId"
+ class="dropdown-item">
+ {{tissue.name}}
+ </a>
+ </div>
</div>
</div>
</div>
- </div>
- </ng-container>
-
- <app-toggle class="footer-buttons" textOn="Drugs" textOff="Off"
- tooltipOn="Display adjacent drugs ON."
- tooltipOff="Display adjacent drugs OFF."
- [smallStyle]="smallStyle"
- [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
-
- <app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Animation On" textOff="Off"
- tooltipOn="Enable the network animation."
- tooltipOff="Disable the network animation and freeze nodes."
- [smallStyle]="smallStyle"
- [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
-
+ </ng-container>
+
+ <app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Drugs" textOff="Off"
+ tooltipOn="Display adjacent drugs ON."
+ tooltipOff="Display adjacent drugs OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
+
+ <app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Animation On" textOff="Off"
+ tooltipOn="Enable the network animation."
+ tooltipOff="Disable the network animation and freeze nodes."
+ [smallStyle]="smallStyle"
+ [value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
+ </div>
</footer>
</div>
</div>
diff --git a/src/styles.scss b/src/styles.scss
index d6ff399d79bc4cd8e2d9b5026ee6afd80aa33bea..ef29e719e04c64858d252fa226fb60610cf235a8 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -15,17 +15,33 @@
.canvas-content {
height: calc(100% - #{$network-footer-height});
+ z-index: $explorer-network-z;
}
+// general network settings, some will be overwritten in analysis
.network-footer-toolbar {
position: absolute;
- overflow-x: auto;
- overflow-y: hidden;
width: 100%;
bottom: 0;
height: $network-footer-height;
+ &-inner-container{
+ width: 100%;
+ display: inline-flex;
+ overflow-x: auto;
+ overflow-y: hidden;
+ height: $network-footer-inner-container-height;
+ position: absolute;
+ bottom: 0;
+ }
&-element {
position: relative;
+ margin-top: calc(#{$network-footer-inner-container-height} - #{$network-footer-height} + #{$network-footer-space-button-to-border});
+ }
+ .dropdown-menu{
+ z-index: $explorer-network-toolbar-dropdown-z;
+ .scroll-area{
+ height: calc(#{$network-footer-inner-container-height} - #{$network-footer-height});
+ }
}
}
@@ -185,7 +201,10 @@ div.covex.explorer {
width: 100%;
position: absolute;
margin-top: 0;
- z-index: 10;
+ z-index: $analysis-view-z;
+ .canvas-content {
+ z-index: $analysis-network-z;
+ }
}
div.field.has-addons.add-remove-toggle {
diff --git a/src/variables.scss b/src/variables.scss
index bf25cef9ccd28356a8b1ae3f21b4a5d78ca452d1..0af86f913ed1e48944cadf86adcee813e4c2f106 100644
--- a/src/variables.scss
+++ b/src/variables.scss
@@ -1,6 +1,15 @@
$row-data-selector-height: auto;
$network-header-height: 3rem;
$network-footer-height: 4rem;
+$network-footer-inner-container-height: 25rem;
+$network-footer-space-button-to-border: 0.5rem;
+
+$explorer-network-z: 10;
+$explorer-network-toolbar-dropdown-z: 20;
+
+$analysis-view-z: 30;
+$analysis-network-z: 40;
+$analysis-network-toolbar-dropdown-z: 50;
$analysis-tab-header-height: 2.5rem;
$analysis-tab-header-padding: 1.5rem;