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Commit 70666c37 authored by Hartung, Michael's avatar Hartung, Michael
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auto network layout until stabilization or 1000 iterations

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src/app/components/analysis-panel/analysis-panel.component.ts
+ 6
− 140
View file @ 70666c37
...@@ -197,6 +197,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit ...@@ -197,6 +197,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options); this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
this.networkHandler.activeNetwork.networkInternal.on('stabilizationIterationsDone', () => {
if (!this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
});
this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneId.startsWith('d')); this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneId.startsWith('d'));
this.tableDrugs.forEach((r) => { this.tableDrugs.forEach((r) => {
r.rawScore = r.score; r.rawScore = r.score;
...@@ -400,80 +406,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit ...@@ -400,80 +406,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
} }
} }
// public saveAddNodes(nodeList: Node[]) {
// const existing = this.nodeData.nodes.get().map(n => n.id);
// const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1)
// this.nodeData.nodes.add(toAdd);
// }
// public saveRemoveDisorders(nodeList: Node[]) {
// const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
// if (other == null)
// this.nodeData.nodes.remove(nodeList);
// else {
// const otherIds = other.map(d => d.id);
// const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1)
// this.nodeData.nodes.remove(rest)
// }
// }
// public updateAdjacentProteinDisorders(bool: boolean) {
// this.adjacentDisordersProtein = bool;
// if (this.adjacentDisordersProtein) {
// this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins').subscribe(response => {
// for (const interaction of response.edges) {
// const edge = {from: interaction.protein, to: interaction.disorder};
// this.adjacentProteinDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
// disorder.id = disorder.drugstoneId;
// this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
// }
// this.saveAddNodes(this.adjacentProteinDisorderList);
// this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
// this.emitVisibleItems(true);
// });
// this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
// } else {
// this.saveRemoveDisorders(this.adjacentProteinDisorderList);
// this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
// this.adjacentProteinDisorderList = [];
// this.adjacentProteinDisorderEdgesList = [];
// this.legendContext = this.adjacentDisordersDrug ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
// this.emitVisibleItems(true);
// }
// }
// public updateAdjacentDrugDisorders(bool: boolean) {
// this.adjacentDisordersDrug = bool;
// if (this.adjacentDisordersDrug) {
// this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs').subscribe(response => {
// for (const interaction of response.edges) {
// const edge = {from: interaction.drug, to: interaction.disorder};
// this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
// disorder.id = disorder.drugstoneId;
// this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
// }
// this.saveAddNodes(this.adjacentDrugDisorderList);
// this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
// this.emitVisibleItems(true);
// });
// this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
// } else {
// this.saveRemoveDisorders(this.adjacentDrugDisorderList);
// this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
// this.adjacentDrugDisorderList = [];
// this.adjacentDrugDisorderEdgesList = [];
// this.legendContext = this.adjacentDisordersProtein ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
// this.emitVisibleItems(true);
// }
// }
public downloadLink(view: string): string { public downloadLink(view: string): string {
return `${environment.backend}task_result/?token=${this.token}&view=${view}&fmt=csv`; return `${environment.backend}task_result/?token=${this.token}&view=${view}&fmt=csv`;
} }
...@@ -589,72 +521,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit ...@@ -589,72 +521,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}; };
} }
// hasDrugsLoaded(): boolean {
// if (this.nodeData == null || this.nodeData.nodes == null)
// return false;
// return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.drugstoneId.startsWith('dr')).length > 0;
// }
// public updateAdjacentDrugs(bool: boolean) {
// this.adjacentDrugs = bool;
// if (this.adjacentDrugs) {
// this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
// for (const interaction of response.pdis) {
// const edge = {from: interaction.protein, to: interaction.drug};
// this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
// }
// for (const drug of response.drugs) {
// drug.group = 'foundDrug';
// drug.id = getDrugNodeId(drug)
// this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
// }
// this.nodeData.nodes.add(this.adjacentDrugList);
// this.nodeData.edges.add(this.adjacentDrugEdgesList);
// this.emitVisibleItems(true);
// })
// this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDrugsAndDisorders' : 'adjacentDrugs';
// } else {
// this.nodeData.nodes.remove(this.adjacentDrugList);
// this.nodeData.edges.remove(this.adjacentDrugEdgesList);
// this.adjacentDrugList = [];
// this.adjacentDrugEdgesList = [];
// this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDisorders' : 'explorer';
// this.emitVisibleItems(true);
// }
// }
// public updatePhysicsEnabled(bool: boolean) {
// this.drugstoneConfig.config.physicsOn = bool;
// this.networkHandler.activeNetwork.networkInternal.setOptions({
// physics: {
// enabled: this.drugstoneConfig.config.physicsOn,
// stabilization: {
// enabled: false,
// },
// }
// });
// }
// public toImage() {
// this.downloadDom(this.networkWithLegendEl.nativeElement).catch(error => {
// console.error("Falling back to network only screenshot. Some components seem to be inaccessable, most likely the legend is a custom image with CORS access problems on the host server side.")
// this.downloadDom(this.networkHandler.activeNetwork.networkEl.nativeElement).catch(e => {
// console.error("Some network content seems to be inaccessable for saving as a screenshot. This can happen due to custom images used as nodes. Please ensure correct CORS accessability on the images host server.")
// console.error(e)
// });
// });
// }
// public downloadDom(dom: object) {
// return domtoimage.toPng(dom, {bgcolor: '#ffffff'}).then((generatedImage) => {
// const a = document.createElement('a');
// a.href = generatedImage;
// a.download = `Network.png`;
// a.click();
// });
// }
public tableProteinSelection = (e): void => { public tableProteinSelection = (e): void => {
const oldSelection = [...this.tableSelectedProteins]; const oldSelection = [...this.tableSelectedProteins];
this.tableSelectedProteins = e; this.tableSelectedProteins = e;
......
src/app/network-settings.ts
+ 2
− 1
View file @ 70666c37
...@@ -56,7 +56,8 @@ export class NetworkSettings { ...@@ -56,7 +56,8 @@ export class NetworkSettings {
length: 250 length: 250
}; };
private static mainPhysics = { private static mainPhysics = {
enabled: false enabled: true,
stabilization: true
}; };
static getOptions(network: 'main' | 'analysis' | 'analysis-big', physicsOn) { static getOptions(network: 'main' | 'analysis' | 'analysis-big', physicsOn) {
......
src/app/pages/explorer-page/explorer-page.component.ts
+ 6
− 0
View file @ 70666c37
...@@ -282,6 +282,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { ...@@ -282,6 +282,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options); this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
this.networkHandler.activeNetwork.networkInternal.on('stabilizationIterationsDone', () => {
if (!this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
});
if (!this.drugstoneConfig.config.showSidebar) { if (!this.drugstoneConfig.config.showSidebar) {
// skip network options for selecting nodes when there are no options to use it // skip network options for selecting nodes when there are no options to use it
return return
......
src/index.html
+ 1
− 1
View file @ 70666c37
...@@ -51,7 +51,7 @@ ...@@ -51,7 +51,7 @@
<drugst-one id="netexp1" <drugst-one id="netexp1"
pluginId="2" 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":"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='{"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}' config='{"physicsOn":false,"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
network='{"nodes":[{"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":"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> </drugst-one>
......
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