From b090bab98462d1b5028bc0429e3903326dee19e3 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Thu, 22 Sep 2022 11:27:26 +0200
Subject: [PATCH] small changes
---
src/app/components/network/network.component.ts | 10 +++++-----
src/app/config.ts | 8 +++++---
src/app/interfaces.ts | 3 +--
.../network-handler/network-handler.service.ts | 2 +-
src/index.html | 6 +++++-
5 files changed, 17 insertions(+), 12 deletions(-)
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 27e6776b..b4dd056b 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -4,11 +4,10 @@ import {InteractionDatabase} from 'src/app/config';
import {DrugstoneConfigService} from 'src/app/services/drugstone-config/drugstone-config.service';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
import {OmnipathControllerService} from 'src/app/services/omnipath-controller/omnipath-controller.service';
-import {mapCustomEdge, mapCustomNode, mapNetexEdge, ProteinNetwork} from '../../main-network';
+import {mapCustomEdge, mapCustomNode} from '../../main-network';
import {
getDrugNodeId,
getWrapperFromNode,
- LegendContext,
Node,
NodeData,
NodeAttributeMap,
@@ -21,7 +20,7 @@ import {AnalysisService} from 'src/app/services/analysis/analysis.service';
import {NetworkSettings} from 'src/app/network-settings';
import {pieChartContextRenderer} from 'src/app/utils';
import {NetworkHandlerService} from 'src/app/services/network-handler/network-handler.service';
-import {LegendService} from "../../services/legend-service/legend-service.service";
+import {LegendService} from 'src/app/services/legend-service/legend-service.service';
@Component({
@@ -81,16 +80,17 @@ export class NetworkComponent implements OnInit {
public nodeRenderer = null;
- constructor(public legendService: LegendService, public networkHandler: NetworkHandlerService, public analysis: AnalysisService, public drugstoneConfig: DrugstoneConfigService, public netex: NetexControllerService, public omnipath: OmnipathControllerService) {
+ constructor(public configService: DrugstoneConfigService, public legendService: LegendService, public networkHandler: NetworkHandlerService, public analysis: AnalysisService, public drugstoneConfig: DrugstoneConfigService, public netex: NetexControllerService, public omnipath: OmnipathControllerService) {
}
ngOnInit(): void {
this.networkHandler.networks[this.networkType] = this;
+ this.networkSidebarOpen = this.configService.config.expandNetworkMenu || false;
}
async getInteractions(key: InteractionDatabase) {
let edges = [];
- if (key == 'omnipath') {
+ if (key === 'omnipath') {
const names = this.nodeData.nodes.map((node) => node.label);
const nameToNetworkId = {};
this.nodeData.nodes.map((node) => nameToNetworkId[node.label] = node.id);
diff --git a/src/app/config.ts b/src/app/config.ts
index bd6112e2..abee66b7 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -1,4 +1,4 @@
-import { AlgorithmTarget, AlgorithmType, QuickAlgorithmType } from "./interfaces";
+import { AlgorithmTarget, AlgorithmType, QuickAlgorithmType } from './interfaces';
// https://visjs.github.io/vis-network/docs/network/nodes.html
export interface NodeGroup {
@@ -52,6 +52,7 @@ export interface IConfig {
showTasks: boolean;
showSelection: boolean;
showNetworkMenu: false | 'left' | 'right';
+ expandNetworkMenu: boolean;
showNetworkMenuButtonExpression: boolean;
showNetworkMenuButtonScreenshot: boolean;
showNetworkMenuButtonExportGraphml: boolean;
@@ -82,7 +83,7 @@ export interface IConfig {
identifier?: Identifier;
nodeShadow?: boolean;
edgeShadow?: boolean;
- algorithms: { [key in AlgorithmTarget]: Array<AlgorithmType | QuickAlgorithmType> }
+ algorithms: { [key in AlgorithmTarget]: Array<AlgorithmType | QuickAlgorithmType> };
}
@@ -144,6 +145,7 @@ export const defaultConfig: IConfig = {
showTasks: true,
showNetworkMenu: 'right',
showLegend: true,
+ expandNetworkMenu: false,
showNetworkMenuButtonExpression: true,
showNetworkMenuButtonScreenshot: true,
showNetworkMenuButtonExportGraphml: true,
@@ -170,7 +172,7 @@ export const defaultConfig: IConfig = {
edgeShadow: true,
licensedDatasets: false,
algorithms: {
- 'drug': ['trustrank', 'closeness', 'degree', 'proximity'],
+ drug: ['trustrank', 'closeness', 'degree', 'proximity'],
'drug-target': ['trustrank', 'multisteiner', 'keypathwayminer', 'degree', 'closeness', 'betweenness']
},
nodeGroups: {
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 820c9d75..0a389527 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -47,8 +47,7 @@ export type NodeType= 'protein' | 'drug' | 'disorder' | 'other'
export type NetworkType = 'explorer' | 'analysis'
-export type LegendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
- 'seeds' | 'adjacentDisorders';
+export type LegendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' | 'seeds' | 'adjacentDisorders';
/// drugstoneId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
diff --git a/src/app/services/network-handler/network-handler.service.ts b/src/app/services/network-handler/network-handler.service.ts
index db2496cd..ab41f624 100644
--- a/src/app/services/network-handler/network-handler.service.ts
+++ b/src/app/services/network-handler/network-handler.service.ts
@@ -19,7 +19,7 @@ export class NetworkHandlerService {
private change = new Subject<any>();
public networks: { NetworkType: NetworkComponent } | {} = {};
- public activeNetwork: NetworkComponent = new NetworkComponent(this.legendService, this.networkHandler, this.analysis, this.drugstoneConfig, this.netex, this.omnipath);
+ public activeNetwork: NetworkComponent = new NetworkComponent(this.drugstoneConfig, this.legendService, this.networkHandler, this.analysis, this.drugstoneConfig, this.netex, this.omnipath);
public setActiveNetwork(network: NetworkType) {
this.triggerChange();
diff --git a/src/index.html b/src/index.html
index e77521a3..77d89d18 100644
--- a/src/index.html
+++ b/src/index.html
@@ -93,7 +93,7 @@
<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]}}}'
- config='{"showSimpleAnalysis": true, "licensedDatasets": false, "physicsOn":false,"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":true,"showLegend":true}'
+ 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"}]}'
>
</drugst-one>
@@ -214,3 +214,7 @@
</script>
</body>
</html>
+<style>
+ /*:root {--drgstn-font-family: Oxygen}*/
+</style>
+
--
GitLab