From 2ec113fc326399415d3af45c3477804617059aa9 Mon Sep 17 00:00:00 2001
From: Michael Hartung <michi@Michaels-MacBook-Pro.local>
Date: Fri, 23 Jul 2021 16:08:10 +0200
Subject: [PATCH] handling of multiple ensg numbers for same gene
---
.../analysis-panel.component.ts | 1 +
.../explorer-page/explorer-page.component.ts | 36 +++++++++++--------
src/app/utils.ts | 15 ++++++++
src/index.html | 4 +--
4 files changed, 40 insertions(+), 16 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 6eeec400..1a7b525b 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -31,6 +31,7 @@ import {NetworkSettings} from '../../network-settings';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
import {defaultConfig, IConfig} from 'src/app/config';
import { mapCustomEdge, mapCustomNode } from 'src/app/main-network';
+import { removeDuplicateObjectsFromList } from 'src/app/utils';
declare var vis: any;
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 4528fa49..e190b0d2 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -23,7 +23,7 @@ import domtoimage from 'dom-to-image';
import {NetworkSettings} from '../../network-settings';
import {defaultConfig, EdgeGroup, IConfig, InteractionDatabase, NodeGroup} from '../../config';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
-import {rgbaToHex, rgbToHex, standardize_color} from '../../utils'
+import {removeDuplicateObjectsFromList, rgbaToHex, rgbToHex, standardize_color} from '../../utils'
import * as merge from 'lodash/fp/merge';
// import * as 'vis' from 'vis-network';
@@ -272,27 +272,37 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (network.nodes.length) {
network.nodes = await this.netex.mapNodes(network.nodes, this.myConfig.identifier);
}
+
+ if (this.myConfig.identifier === 'ensg') {
+ // remove possible duplicate IDs
+ network.nodes = removeDuplicateObjectsFromList(network.nodes, 'netexId');
+ }
+
// at this point, we have nodes synched with the backend
// use netexIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
- const seenNodeIds = new Set();
- network.nodes.forEach((node, index, object) => {
- if (seenNodeIds.has(node.id)) {
- // remove duplicate ensg nodes, TODO is there a better way to do this?
- object.splice(index, 1);
- return;
- } else {
- seenNodeIds.add(node.id);
- }
- nodeIdMap[node.id] = node.netexId ? node.netexId : node.id;
+
+ 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.netexId ? node.netexId : node.id;
node.id = nodeIdMap[node.id];
});
- // adjust edge labels accordingly
+
+ // adjust edge labels accordingly and filter
+ const edges = new Array();
network.edges.forEach(edge => {
edge.from = nodeIdMap[edge.from];
edge.to = nodeIdMap[edge.to];
+ // check if edges have endpoints
+ if (edge.from !== undefined && edge.to !== undefined) {
+ edges.push(edge);
+ }
});
+ // remove edges without endpoints
+ network.edges = edges;
+
this.proteins = network.nodes;
this.edges = network.edges;
}
@@ -534,8 +544,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
nodeGroups = merge(defaultNodeGroups, nodeGroups);
// overwrite default node groups
this.myConfig[key] = nodeGroups;
- console.log('nodeGroups after preprocessing')
- console.log(nodeGroups)
}
/**
diff --git a/src/app/utils.ts b/src/app/utils.ts
index c2406510..72b2bff4 100644
--- a/src/app/utils.ts
+++ b/src/app/utils.ts
@@ -1,5 +1,7 @@
// From https://stackoverflow.com/a/27709336/3850564
+import { Node } from "./interfaces";
+
export function getGradientColor(startColor: string, endColor: string, percent: number) {
// strip the leading # if it's there
startColor = startColor.replace(/^\s*#|\s*$/g, '');
@@ -104,3 +106,16 @@ export function standardize_color(str){
return ctx.fillStyle.toString();
}
+export function removeDuplicateObjectsFromList(nodes: Node[], attribute: string): Node[] {
+ const seenIds = new Set();
+ const filteredArray = new Array();
+ for (const node of nodes) {
+ if (seenIds.has(node[attribute])) {
+ continue;
+ }
+ filteredArray.push(node);
+ seenIds.add(node[attribute]);
+ }
+ return filteredArray;
+}
+
diff --git a/src/index.html b/src/index.html
index c1d46c92..5c5e6a18 100644
--- a/src/index.html
+++ b/src/index.html
@@ -37,10 +37,10 @@
config='{
"nodeGroups": {"selectedNode": {"font": {"size": "18"} }, "0.5": {"font": "18px verdana blue", "type": "0.5er Instanz", "color": "green", "groupName": "0.5", "shape": "star"}, "patientgroup": {"type": "Patient", "detailShowLabel": "true", "color": "#632345", "groupName": "patient group", "shape": "dot", "size": "50"}, "pugGroup": {"type": "woof woof", "color": "grey", "groupName": "Pug Group", "shape": "triangle", "image": "https://static.raymondcamden.com/images/2016/11/pug.png"}},
"edgeGroups": {"xxx": {"color": "black", "groupName": "xxx Group", "dashes": [1, 2]}, "notdashes": {"color": "black", "groupName": "not dashes Group"}},
- "identifier": "symbol"
+ "identifier": "ensg"
}'
network='{
- "nodes": [{"id": "MYC", "label": "node w/o group"}, {"id": "TP53", "group": "0.5"}, {"id": "C5", "group": "pugGroup"}, {"id": "Patient No. 5", "group": "patientgroup"}, {"label": "PTEN", "id": "PTEN", "group": 0.5, "value":"5"}],
+ "nodes": [{"id": "ENSG00000171862", "label": "node w/o group"}, {"id": "ENSG00000284792", "group": "0.5"}, {"id": "ENSG00000106804", "group": "pugGroup"}, {"id": "Patient No. 5", "group": "patientgroup"}, {"label": "PTEN", "id": "PTEN", "group": 0.5, "value":"5"}],
"edges": [
{"from": "TP53","to": "C5","group": "xxx", "label": "this is a label", "title": "this is a title"},
{"from": "Patient No. 5","to": "C5","label": "w/o group"}
--
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