From 7f6059103ba1e00a2b3dd44536e49938bcf1cfdd Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 4 Nov 2022 21:01:17 +0100
Subject: [PATCH] added tissue based tmp normalization
---
.../components/info-tile/info-tile.component.html | 4 ++--
src/app/components/network/network.component.ts | 14 ++++++++++----
.../netex-controller/netex-controller.service.ts | 7 +++++++
3 files changed, 19 insertions(+), 6 deletions(-)
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 9b1cf0a4..5906f7e2 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -72,11 +72,11 @@
*ngIf="getExpressionScore() != null"
[ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }"
>
- <b><span>Expression:</span></b>
+ <b><span>Median tissue expression (TPM):</span></b>
<span class="is-capitalized"> {{ getExpressionScore() | number }}</span>
<span
class="icon has-text-info"
- pTooltip="Tissue expression data is provided by the GTEx project. Unit is transcript per million."
+ pTooltip="Median expression data is provided by the GTEx project. Unit is TPM (transcript per million)."
[tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
tooltipPosition="left"
>
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index fbd90923..5487e379 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -426,7 +426,7 @@ export class NetworkComponent implements OnInit {
proteinNodes.push(element);
}
});
- this.netex.tissueExpressionGenes(this.selectedTissue, proteinNodes).subscribe((response) => {
+ this.netex.tissueExpressionGenes(this.selectedTissue, proteinNodes).subscribe(async (response) => {
this.expressionMap = response;
const updatedNodes = [];
this.nodeRenderer = pieChartContextRenderer;
@@ -443,7 +443,13 @@ export class NetworkComponent implements OnInit {
});
}
});
- const maxExpr = Math.max(...Object.values(this.expressionMap));
+ let maxExpr = 1_000_000;
+ await this.netex.maxTissueExpression(this.selectedTissue).then(response => {
+ maxExpr = response.max;
+ }).catch(err => {
+ console.error(err);
+ maxExpr = Math.max(...Object.values(this.expressionMap));
+ });
const exprMap = {};
for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
networkIdMapping[drugstoneId].forEach(networkId => {
@@ -501,7 +507,7 @@ export class NetworkComponent implements OnInit {
}
public getGradient(nodeId: string) {
- return (Object.keys(this.gradientMap).length && this.gradientMap[nodeId] != null) ? this.gradientMap[nodeId] : 1.0;
+ return (Object.keys(this.gradientMap).length && this.gradientMap[nodeId] != null) ? this.gradientMap[nodeId] : 1.0;
}
/**
@@ -542,7 +548,7 @@ export class NetworkComponent implements OnInit {
this.nodeRenderer
)
),
- updatedNodes.push(node);
+ updatedNodes.push(node);
}
this.nodeData.nodes.update(updatedNodes);
this.loadingScreen.stateUpdate(false);
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index f4aa4e37..e54280e5 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -47,6 +47,13 @@ export class NetexControllerService {
return this.http.post('https://api.digest-validation.net/set', payload).toPromise();
}
+ public maxTissueExpression(tissue: Tissue): Promise<any> {
+ const params = new HttpParams()
+ .set('tissue', tissue.drugstoneId);
+ return this.http.get(environment.backend + 'tissue_max_expression/', {params}).toPromise();
+ }
+
+
public tissueExpressionGenes(tissue: Tissue, nodes: Node[]): Observable<any> {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
--
GitLab