From 5ed12043991f693460773558f5a15062c8e3af4c Mon Sep 17 00:00:00 2001
From: "Hartung, Michael" <michael.hartung@uni-hamburg.de>
Date: Mon, 11 Jul 2022 16:10:49 +0200
Subject: [PATCH] fix node duplication bug when node group has "id" and make
enrichment analysis button small style
---
.../analysis-panel.component.ts | 40 +++++++++----------
.../info-tile/info-tile.component.html | 2 +-
.../network-menu-left.component.html | 4 +-
.../network-menu/network-menu.component.html | 4 +-
.../components/network/network.component.ts | 20 +++++-----
.../add-expressed-proteins.component.ts | 4 +-
.../launch-analysis.component.ts | 4 +-
src/app/interfaces.ts | 21 +++++-----
src/app/network-settings.ts | 1 +
.../explorer-page.component.html | 4 +-
.../explorer-page/explorer-page.component.ts | 27 ++++++++-----
.../netex-controller.service.ts | 10 ++---
src/index.html | 29 ++++++++++++--
13 files changed, 100 insertions(+), 70 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 59584070..3b5c1419 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -197,12 +197,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.tableDrugs = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('d'));
+ this.tableDrugs = nodes.filter( e => e.netexId && e.netexId.startsWith('d'));
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
});
- this.tableProteins = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('p'));
+ this.tableProteins = nodes.filter( e => e.netexId && e.netexId.startsWith('p'));
this.tableSelectedProteins = [];
this.tableProteins.forEach((r) => {
r.rawScore = r.score;
@@ -233,7 +233,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.nodeType === 'drug' || node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
+ if (node.nodeType === 'drug' || node.netexId === undefined || !node.netexId.startsWith('p')) {
return;
}
const wrapper = getWrapperFromNode(node);
@@ -306,7 +306,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.nodeData.nodes.forEach((node) => {
// let drugType;
// let drugInTrial;
- // if (node.drugstoneId && node.drugstoneId.startsWith('d')) {
+ // if (node.netexId && node.netexId.startsWith('d')) {
// drugType = node.status;
// drugInTrial = node.inTrial;
// }
@@ -428,7 +428,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
- // disorder.id = disorder.drugstoneId;
+ // disorder.id = disorder.netexId;
// this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
// }
// this.saveAddNodes(this.adjacentProteinDisorderList);
@@ -456,7 +456,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
- // disorder.id = disorder.drugstoneId;
+ // disorder.id = disorder.netexId;
// this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
// }
// this.saveAddNodes(this.adjacentDrugDisorderList);
@@ -495,9 +495,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public inferNodeGroup(wrapper: Wrapper): string {
if (wrapper.data.group !== undefined) {
return wrapper.data.group;
- } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('d')) {
+ } else if (wrapper.data.netexId !== undefined && wrapper.data.netexId.startsWith('d')) {
return 'drug';
- } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('p')) {
+ } else if (wrapper.data.netexId !== undefined && wrapper.data.netexId.startsWith('p')) {
return 'protein';
}
}
@@ -531,7 +531,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public createNetwork(result: any): { edges: any[], nodes: any[] } {
const config = result.parameters.config;
this.myConfig = config;
-
+
const identifier = this.myConfig.identifier;
// add drugGroup and foundNodesGroup for added nodes
@@ -554,14 +554,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// convert id to netex Id if exists
const nodeDetails = details[node];
- nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.drugstoneId;
- if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('p')) {
+ nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.netexId;
+ if (nodeDetails.netexId && nodeDetails.netexId.startsWith('p')) {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'foundNode';
nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
this.proteins.push(nodeDetails);
- } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('d')) {
+ } else if (nodeDetails.netexId && nodeDetails.netexId.startsWith('d')) {
// node is drug, was found during analysis
nodeDetails.type = 'Drug';
nodeDetails.group = 'foundDrug';
@@ -586,7 +586,7 @@ 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;
+ // return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
// }
// public updateAdjacentDrugs(bool: boolean) {
@@ -684,7 +684,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// this.selectedTissue = null;
// const updatedNodes = [];
// for (const item of this.proteins) {
- // if (item.drugstoneId === undefined) {
+ // if (item.netexId === undefined) {
// // nodes that are not mapped to backend remain untouched
// continue;
// }
@@ -718,7 +718,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// // filter out non-proteins, e.g. drugs
// const proteinNodes = [];
// this.nodeData.nodes.forEach(element => {
- // if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
+ // if (element.id.startsWith('p') && element.netexId !== undefined) {
// proteinNodes.push(element);
// }
// });
@@ -728,17 +728,17 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// // mapping from netex IDs to network IDs, TODO check if this step is necessary
// const networkIdMappping = {}
// this.nodeData.nodes.forEach(element => {
- // networkIdMappping[element.drugstoneId] = element.id
+ // networkIdMappping[element.netexId] = element.id
// });
// const maxExpr = Math.max(...Object.values(this.expressionMap));
- // for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
- // const networkId = networkIdMappping[drugstoneId]
+ // for (const [netexId, expressionlvl] of Object.entries(this.expressionMap)) {
+ // const networkId = networkIdMappping[netexId]
// const node = this.nodeData.nodes.get(networkId);
// if (node === null) {
// continue;
// }
// const wrapper = getWrapperFromNode(node)
- // this.gradientMap[drugstoneId] = 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.networkHandler.activeNetwork.networkInternal.getPositions([networkId]);
// node.x = pos[networkId].x;
// node.y = pos[networkId].y;
@@ -749,7 +749,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// this.myConfig,
// isSeed,
// this.analysis.inSelection(wrapper),
- // this.gradientMap[drugstoneId]));
+ // this.gradientMap[netexId]));
// node.shape = 'custom';
// node.ctxRenderer = pieChartContextRenderer;
// updatedNodes.push(node);
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index dc8f22f3..744580ef 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -101,7 +101,7 @@
</div>
<app-toggle
- *ngIf="wrapper.data.drugstoneId && wrapper.data.drugstoneId.startsWith('p')"
+ *ngIf="wrapper.data.netexId && wrapper.data.netexId.startsWith('p')"
[value]="analysis.inSelection(wrapper)"
(valueChange)="
$event ? analysis.addItems([wrapper]) : analysis.removeItems([wrapper])
diff --git a/src/app/components/network/network-menu-left/network-menu-left.component.html b/src/app/components/network/network-menu-left/network-menu-left.component.html
index 16d61492..c251083c 100644
--- a/src/app/components/network/network-menu-left/network-menu-left.component.html
+++ b/src/app/components/network/network-menu-left/network-menu-left.component.html
@@ -151,8 +151,8 @@
(click)="networkHandler.activeNetwork.selectTissue(tissue)"
[class.is-active]="
networkHandler.activeNetwork.selectedTissue &&
- tissue.drugstoneId ===
- networkHandler.activeNetwork.selectedTissue.drugstoneId
+ tissue.netexId ===
+ networkHandler.activeNetwork.selectedTissue.netexId
"
class="dropdown-item"
>
diff --git a/src/app/components/network/network-menu/network-menu.component.html b/src/app/components/network/network-menu/network-menu.component.html
index 4a80fc1d..f529997a 100644
--- a/src/app/components/network/network-menu/network-menu.component.html
+++ b/src/app/components/network/network-menu/network-menu.component.html
@@ -151,8 +151,8 @@
(click)="networkHandler.activeNetwork.selectTissue(tissue)"
[class.is-active]="
networkHandler.activeNetwork.selectedTissue &&
- tissue.drugstoneId ===
- networkHandler.activeNetwork.selectedTissue.drugstoneId
+ tissue.netexId ===
+ networkHandler.activeNetwork.selectedTissue.netexId
"
class="dropdown-item"
>
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 529f5fcc..9410c3d9 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -73,7 +73,7 @@ export class NetworkComponent implements OnInit {
public highlightSeeds = false;
public seedMap: NodeAttributeMap = {};
- // keys are node drugstoneIds
+ // keys are node netexIds
public expressionMap: NodeAttributeMap = {};
public gradientMap: NodeAttributeMap = {};
@@ -119,7 +119,7 @@ export class NetworkComponent implements OnInit {
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
- disorder.id = disorder.drugstoneId;
+ disorder.id = disorder.netexId;
this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.config))
}
this.saveAddNodes(this.adjacentProteinDisorderList);
@@ -147,7 +147,7 @@ export class NetworkComponent implements OnInit {
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
- disorder.id = disorder.drugstoneId;
+ disorder.id = disorder.netexId;
this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.config));
}
this.saveAddNodes(this.adjacentDrugDisorderList);
@@ -271,7 +271,7 @@ export class NetworkComponent implements OnInit {
const updatedNodes = [];
// for (const item of this.proteins) {
for (const item of this.currentViewProteins) {
- if (item.drugstoneId === undefined) {
+ if (item.netexId === undefined) {
// nodes that are not mapped to backend remain untouched
continue;
}
@@ -303,7 +303,7 @@ export class NetworkComponent implements OnInit {
// filter out non-proteins, e.g. drugs
const proteinNodes = [];
this.nodeData.nodes.forEach(element => {
- if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
+ if (element.id.startsWith('p') && element.netexId !== undefined) {
proteinNodes.push(element);
}
});
@@ -313,11 +313,11 @@ export class NetworkComponent implements OnInit {
// mapping from netex IDs to network IDs, TODO check if this step is necessary
const networkIdMappping = {}
this.nodeData.nodes.forEach(element => {
- networkIdMappping[element.drugstoneId] = element.id
+ networkIdMappping[element.netexId] = element.id
});
const maxExpr = Math.max(...Object.values(this.expressionMap));
- for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
- const networkId = networkIdMappping[drugstoneId]
+ for (const [netexId, expressionlvl] of Object.entries(this.expressionMap)) {
+ const networkId = networkIdMappping[netexId]
const node = this.nodeData.nodes.get(networkId);
if (node === null) {
continue;
@@ -349,7 +349,7 @@ export class NetworkComponent implements OnInit {
public 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;
+ return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
}
public setLegendContext() {
@@ -376,7 +376,7 @@ export class NetworkComponent implements OnInit {
this.highlightSeeds = bool;
const updatedNodes = [];
for (const item of this.currentViewProteins) {
- if (item.drugstoneId === undefined) {
+ if (item.netexId === undefined) {
// nodes that are not mapped to backend remain untouched
continue;
}
diff --git a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
index c1e8a59c..634873da 100644
--- a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
+++ b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
@@ -39,7 +39,7 @@ export class AddExpressedProteinsComponent implements OnChanges {
public async addProteins() {
this.loading = true;
const result = await this.http.post<any>(`${environment.backend}query_tissue_proteins/`,
- {tissueId: this.selectedTissue.drugstoneId, threshold: this.threshold}).toPromise();
+ {tissueId: this.selectedTissue.netexId, threshold: this.threshold}).toPromise();
const items = [];
for (const detail of result) {
items.push(getWrapperFromNode(detail));
@@ -59,7 +59,7 @@ export class AddExpressedProteinsComponent implements OnChanges {
if (!this.currentViewProteins || this.expressionMap === undefined) {
return;
}
- this.proteins = this.currentViewProteins.filter(p => this.expressionMap[p.drugstoneId] >= threshold);
+ this.proteins = this.currentViewProteins.filter(p => this.expressionMap[p.netexId] >= threshold);
}
public close() {
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index bf4637eb..38ef3ecd 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -104,8 +104,8 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
public async startTask() {
- // all nodes in selection have drugstoneId, hence exist in the backend
- const seeds = this.analysis.getSelection().map((item) => item.data.drugstoneId)
+ // all nodes in selection have netexId, hence exist in the backend
+ const seeds = this.analysis.getSelection().map((item) => item.data.netexId)
const seedsFiltered = seeds.filter(function (el) {
return el != null;
});
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 59daa8bf..e479edf3 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -5,7 +5,7 @@ export interface Node {
symbol: string;
id: string;
type: string;
- drugstoneId?: string;
+ netexId?: string;
drugId?:string;
uniprotAc?: string;
ensg?: Array<string>;
@@ -28,7 +28,7 @@ export interface Node {
}
export interface Tissue {
- drugstoneId: number;
+ netexId: number;
name: string;
}
@@ -42,7 +42,7 @@ export type NetworkType = 'explorer' | 'analysis'
export type LegendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders' | 'adjacentDrugsAndDisorders';
-/// drugstoneId to expressionlvl
+/// netexId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
export interface NetexInteraction {
@@ -125,21 +125,21 @@ export function getDrugNodeId(drug: Drug) {
/**
* Returns backend_id of Drug object
*/
- return drug.drugstoneId
+ return drug.netexId
}
// export function getDisorderNodeId(disorder: Disorder) {
// /**
// * Returns backend_id of Drug object
// */
-// return disorder.drugstoneId
+// return disorder.netexId
export function getNodeId(node: Node) {
/**
* Returns backend_id of Gene object
*/
- // if ('drugstoneId' in node) {
- // return node['drugstoneId']
+ // if ('netexId' in node) {
+ // return node['netexId']
// } else {
// return node.id
// }
@@ -150,7 +150,7 @@ export function getNetworkId(node: Node) {
/**
* Returns ID of a network node
*/
- return node.drugstoneId
+ return node.netexId
}
export function getId(gene: Node) {
@@ -165,6 +165,7 @@ export function getWrapperFromNode(node: Node): Wrapper {
* Constructs wrapper interface for gene
*/
// if node does not have property group, it was custom node from user
+ console.log(node.groupName)
node.group = node.group ? node.group : 'default';
node.label = node.label ? node.label : node.id
return {
@@ -182,7 +183,7 @@ export interface Wrapper {
label: string;
type?: string;
symbol?: string;
- drugstoneId?: string;
+ netexId?: string;
ensg?: Array<string>;
shape?: string;
color?: string;
@@ -215,7 +216,7 @@ export interface Drug {
inTrial: boolean;
inLiterature: boolean;
trialLinks: string[];
- drugstoneId: string;
+ netexId: string;
group: string;
}
diff --git a/src/app/network-settings.ts b/src/app/network-settings.ts
index ddd420a3..b8e1ae85 100644
--- a/src/app/network-settings.ts
+++ b/src/app/network-settings.ts
@@ -133,6 +133,7 @@ export class NetworkSettings {
} else {
node = merge(node, config.nodeGroups[node.group]);
}
+
// note that seed and selected node style are applied after the node style is fetched.
// this allows to overwrite only attributes of interest, therefor in e.g. seedNode group
// certain attributes like shape can remain undefined
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index c6df3dde..c49b9079 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -465,7 +465,7 @@
*ngIf="analysis.getCount() > 0"
[href]="gProfilerLink()"
target="_blank"
- class="button is-primary is-fullwidth is-rounded has-tooltip"
+ class="button is-primary is-fullwidth is-rounded has-tooltip is-small"
pTooltip="Use enrichment analysis via g:Profiler (external)."
[tooltipStyleClass]="
'drgstn drgstn-tooltip drgstn-tooltip-top'
@@ -484,7 +484,7 @@
<a
*ngIf="analysis.getCount() === 0"
disabled
- class="button is-primary is-fullwidth is-rounded has-tooltip"
+ class="button is-primary is-fullwidth is-rounded has-tooltip is-small"
pTooltip="Use enrichment analysis via g:Profiler (external)."
[tooltipStyleClass]="
'drgstn drgstn-tooltip drgstn-tooltip-top'
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index cf615e66..dae1f7df 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -40,7 +40,7 @@ declare var vis: any;
export class ExplorerPageComponent implements OnInit, AfterViewInit {
- private networkJSON = '{"nodes": [], "edges": []}';
+ private networkJSON = undefined; //'{"nodes": [], "edges": []}'
public _config: string;
@Input()
@@ -65,7 +65,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (network == null) {
return;
}
- this.networkJSON = JSON.stringify(typeof network === 'string' ? JSON5.parse(network) : network);
+ try {
+ this.networkJSON = JSON.stringify(typeof network === 'string' ? JSON5.parse(network) : network);
+ } catch {
+ console.log('ERROR: Failed parsing input network')
+ }
this.activateConfig();
}
@@ -122,7 +126,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public networkHandler: NetworkHandlerService) {
this.showDetails = false;
this.analysis.subscribeList(async (items, selected) => {
-
// return if analysis panel is open or no nodes are loaded
if (this.selectedAnalysisToken || !this.nodeData.nodes) {
return;
@@ -275,7 +278,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (nodeIds != null && nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
+ if (node.netexId === undefined || !node.netexId.startsWith('p')) {
// skip if node is not a protein mapped to backend
return;
}
@@ -345,17 +348,16 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.drugstoneConfig.config.identifier === 'ensg') {
// remove possible duplicate IDs
- network.nodes = removeDuplicateObjectsFromList(network.nodes, 'drugstoneId');
+ network.nodes = removeDuplicateObjectsFromList(network.nodes, 'netexId');
}
// at this point, we have nodes synched with the backend
- // use drugstoneIds where posssible, but use original id as node name if no label given
+ // use netexIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
network.nodes.forEach((node) => {
// set node label to original id before node id will be set to netex id
node.label = node.label ? node.label : node.id;
-
- nodeIdMap[node.id] = node.drugstoneId ? node.drugstoneId : node.id;
+ nodeIdMap[node.id] = node.netexId ? node.netexId : node.id;
node.id = nodeIdMap[node.id];
});
@@ -461,6 +463,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
// implement nodeShadow option, it needs to be set for all nodes or none
group.shadow = this.drugstoneConfig.config.nodeShadow;
+
+ // group must not have id, otherwise node id's would be overwritten which causes duplciates
+ if (group.hasOwnProperty('id')) {
+ delete group['id'];
+ }
});
this.drugstoneConfig.config[key] = nodeGroups;
@@ -494,9 +501,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
gProfilerLink(): string {
- // nodes in selection have drugstoneId
+ // nodes in selection have netexId
const queryString = this.analysis.getSelection()
- .filter(wrapper => wrapper.data.drugstoneId.startsWith('p'))
+ .filter(wrapper => wrapper.data.netexId.startsWith('p'))
.map(wrapper => wrapper.data.uniprotAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index bce39cb1..baa8a588 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -89,9 +89,9 @@ export class NetexControllerService {
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.drugstoneId ? node.drugstoneId.slice(1) : undefined);
+ const genesBackendIds = nodes.map((node: Node) => node.netexId ? node.netexId.slice(1) : undefined);
const params = new HttpParams()
- .set('tissue', tissue.drugstoneId)
+ .set('tissue', tissue.netexId)
.set('proteins', JSON.stringify(genesBackendIds));
return this.http.get(`${environment.backend}tissue_expression/`, {params});
}
@@ -101,10 +101,10 @@ export class NetexControllerService {
const params = {};
if (nodeType === 'proteins') {
// @ts-ignore
- params.proteins = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
+ params.proteins = nodes.map((node: Node) => node.netexId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
} else if (nodeType === 'drugs') {
// @ts-ignore
- params.drugs = nodes.map((node: Node) => node.drugId && node.drugstoneId.startsWith('dr') ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
+ params.drugs = nodes.map((node: Node) => node.drugId && node.netexId.startsWith('dr') ? node.netexId.slice(2) : undefined).filter(id => id != null);
}
return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
}
@@ -114,7 +114,7 @@ export class NetexControllerService {
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
+ const genesBackendIds = nodes.map((node: Node) => node.netexId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
const params = {
pdi_dataset: pdiDataset,
proteins: genesBackendIds
diff --git a/src/index.html b/src/index.html
index 3614e49c..7094e66b 100644
--- a/src/index.html
+++ b/src/index.html
@@ -48,10 +48,31 @@
<div style="max-width: 80vw">
<drugst-one id="netexp1"
- pluginId="2"
- config='{"interactionDrugProtein":"NeDRex", "physicsOn":true, "showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","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]}},"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"}]}'>
- </drugst-one>
+ pluginId="2"
+ config='{"nodeGroups":{
+ "proteinCoding":{"type":"gene","color":{background:"#116466",border:"#000000"} ,"font":{"color":"#000000"},"borderWidth":2,"groupName":"gene","shape":"square", "id":"proteinCoding"},
+ "up":{"type":"gene","color":{background:"#FC6566",border:"#000000"},"font":{"color":"#000000"},"borderWidth":2,"groupName":"up-regulated gene","shape":"square","id":"up"},
+ "down":{"type":"gene","color":{background:"#1158E9",border:"#000000"},"font":{"color":"#000000"},"borderWidth":2,"groupName":"down-regulated gene","shape":"square","id":"down"},
+ "unchanged":{"type":"gene","color":{background:"#A0B89D",border:"#000000"},"font":{"color":"#000000"},"borderWidth":2,"groupName":"unchanged gene","shape":"square","id":"unchanged"},
+ "metMeta":{"type":"metabolite","color":{background:"#E8A87C",border:"#000000"},"font":{"color":"#000000"},"borderWidth":2,"groupName":"metabolite","shape":"dot","id":"metMeta"},
+ "trait":{"type":"trait","color":"#B4CADB","font":{"color":"#000000"},"groupName":"trait","shape":"ellipse","id":"trait"},
+ "traitMeta":{"type":"trait","color":"#8c3d37","font":{"color":"#000000"},"groupName":"traitMeta","shape":"star","id":"traitMeta"},
+ "foundDrug":{"type":"drug","color":"#B186B4","font":{"color":"#000000"},"groupName":"drug","shape":"diamond"},
+ "defaultDisorder":{"type":"disorder","color":"#F0E48C","font":{"color":"#000000"},"groupName":"disorder","shape":"triangle"}
+ },
+ "edgeGroups":{
+ "GENETIC_ASSOCIATION":{"type":"GENETIC_ASSOCIATION", "groupName":"mQTL","color":"#A9A9A9","dashes":false,"arrowStrikethrough":false},
+ "GENETIC_TRAIT_ASSOCIATION":{"type":"GENETIC_TRAIT_ASSOCIATION","groupName":"mQTL","color":"#b4cadb33","dashes":false,"arrowStrikethrough":false},
+ "COABUNDANCE":{"type":"COABUNDANCE","groupName":"coabundance","color":"#5a735a","dashes":false,"arrowStrikethrough":false},
+ "METABOLIC_ASSOCIATION":{"type":"METABOLIC_ASSOCIATION","groupName":"traitQTL/mWAS","color":"#b4cadb33","dashes":false,"arrowStrikethrough":false},
+ "COREGULATION":{"type":"COREGULATION","groupName":"coregulation","color":"#1db81d","dashes":false,"arrowStrikethrough":false},
+ "PARTIAL_CORRELATION":{"type":"PARTIAL_CORRELATION","groupName":"partial correlation","color":"#FFC31E","dashes":false,"arrowStrikethrough":false},
+ "COEXPRESSION":{"type":"COEXPRESSION","groupName":"coexpression","color":"#82B81D","dashes":false,"arrowStrikethrough":false}},
+ "identifier":"symbol","title":"Drugst.one network","sidebarPos":"right","showOverview":true,"nodeShadow":false,"edgeShadow":false,"showLegend":true,
+ "showFooter":true, "showSimpleAnalysis":true,"showAdvAnalysis":true,"showSelection":true,
+ "autofillEdges":false,"physicsOn":true}'
+ network='{"nodes": [{"type": "gene", "id": "ZNF235", "group": "proteinCoding", "shape": "circle", "label": "ZNF235", "x": 45.1427, "y": 183.494915, "value": 43}, {"type": "gene", "color": {"background": "#116466", "border": "#000000"}, "font": {"color": "#000000"}, "border_width": 2, "shape": "square", "id": "CEACAM16", "border_width_selected": 0, "shadow": false, "group": "proteinCoding", "label": "CEACAM16", "x": -257.39927, "y": 500, "value": 39, "scaling.min": 2, "scaling.max": 54, "physics": false}]}'>
+</drugst-one>
</div>
<!--<div >-->
--
GitLab