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Commit d5a83f31 authored by AndiMajore's avatar AndiMajore
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fixed drug existence check and node groups

parent f5e8bcc4
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src/app/components/analysis-panel/analysis-panel.component.ts
+ 13
− 17
View file @ d5a83f31
......@@ -200,10 +200,11 @@ 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.drugstoneType === 'drug');
this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
});
console.log(this.tableDrugs)
this.tableProteins = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'protein');
this.tableSelectedProteins = [];
......@@ -411,7 +412,6 @@ 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
......@@ -424,24 +424,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.effects = [];
const network = result.network;
// const nodeTypes = attributes.nodeTypes || {};
// const isSeed = attributes.isSeed || {};
// const scores = attributes.scores || {};
const details = attributes.details || {};
const nodeIdMap = {}
// const reverseNodeIdMap = {}
// @ts-ignore
Object.entries(details).filter(e => e[1].drugstoneType === 'protein').forEach(e => {
// let id =
// @ts-ignore
e[1].drugstoneId.forEach(id => {
nodeIdMap[id] = e[1][identifier][0]
})
// if (!nodeIdMap[id])
// nodeIdMap[id] = [e[0]]
// else
// nodeIdMap[id].push(e[0])
})
for (const nodeId of Object.keys(details)) {
const nodeDetails = details[nodeId]
......@@ -449,7 +439,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'protein') {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
nodeDetails.group = result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1 ? 'foundNode' : (nodeDetails.group ? nodeDetails.group : 'default' );
// FIXME connectorNodes are not visualized correctly
nodeDetails.group = result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1 ? 'foundNode' : (nodeDetails.group ? nodeDetails.group : 'connectorNode');
console.log(nodeDetails)
nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
nodeDetails.id = nodeDetails[identifier][0] ? nodeDetails[identifier][0] : nodeDetails.id;
this.proteins.push(nodeDetails);
......@@ -464,18 +456,22 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
// further analysis and the button function can be used to highlight seeds
// option to use scores[node] as gradient, but sccores are very small
console.log(nodeDetails)
nodes.push(NetworkSettings.getNodeStyle(nodeDetails as Node, config, false, false, 1))
}
const edges = [];
let uniqEdges = []
for (const edge of network.edges) {
const e = mapCustomEdge(edge, this.myConfig)
e.from = e.from[0] === 'p' ? nodeIdMap[e.from] : e.from
e.to = e.to[0] === 'p' ? nodeIdMap[e.to] : e.to
const hash = e.from + "_" + e.to;
if (uniqEdges.indexOf(hash) === -1) {
uniqEdges.push(hash);
edges.push(e);
}
}
return {
nodes,
edges,
......
src/app/components/network/network.component.ts
+ 7
− 4
View file @ d5a83f31
......@@ -426,9 +426,11 @@ export class NetworkComponent implements OnInit {
}
public hasDrugsLoaded(): boolean {
if (this.nodeData == null || this.nodeData.nodes == null)
if(this.nodeData && this.nodeData.nodes)
for(const node of this.nodeData.nodes.get())
if(node.drugstoneType && node.drugstoneId === 'drug')
return true;
return false;
return this.nodeData.nodes.get().filter((node: Node) => node.drugId).map(node => node.drugstoneId).filter(id => id.startsWith('dr')).length > 0;
}
public setLegendContext() {
......@@ -442,9 +444,10 @@ export class NetworkComponent implements OnInit {
if (this.highlightSeeds) {
this.legendContext = "drugTargetAndSeeds";
} else {
this.legendContext = 'drugTarget'
this.legendContext = 'drugTarget';
}
}
console.log(this.legendContext)
}
/**
......
src/app/config.ts
+ 38
− 31
View file @ d5a83f31
......@@ -79,6 +79,42 @@ export interface IConfig {
edgeShadow?: boolean;
}
const defaultNodeGroup: NodeGroup = {
// this default group is used for default node group values
// and is fallback in case user does not provide any nodeGroup
groupName: 'Default Node Group',
color: {
border: '#FFFF00',
background: '#FFFF00',
highlight: {
border: '#FF0000',
background: '#FF0000'
},
},
shape: 'triangle',
type: 'default type',
detailShowLabel: false,
font: {
color: '#000000',
size: 14,
face: 'arial',
background: undefined,
strokeWidth: 0,
strokeColor: '#ffffff',
align: 'center',
bold: false,
ital: false,
boldital: false,
mono: false,
},
borderWidth: 1,
borderWidthSelected: 2
};
const connectorNodeGroup: NodeGroup = JSON.parse(JSON.stringify(defaultNodeGroup));
connectorNodeGroup.groupName = 'Connector Node';
// @ts-ignore
/**
* Provide default values
*/
......@@ -126,37 +162,7 @@ export const defaultConfig: IConfig = {
nodeGroups: {
// all NodeGroups but the default group must be set, if not provided by the user, they will be taken from here
// IMPORTANT: node color must be hexacode!
default: {
// this default group is used for default node group values
// and is fallback in case user does not provide any nodeGroup
groupName: 'Default Node Group',
color: {
border: '#FFFF00',
background: '#FFFF00',
highlight: {
border: '#FF0000',
background: '#FF0000'
},
},
shape: 'triangle',
type: 'default type',
detailShowLabel: false,
font: {
color: '#000000',
size: 14,
face: 'arial',
background: undefined,
strokeWidth: 0,
strokeColor: '#ffffff',
align: 'center',
bold: false,
ital: false,
boldital: false,
mono: false,
},
borderWidth: 1,
borderWidthSelected: 2
},
default: defaultNodeGroup,
foundNode: {
groupName: 'Found Nodes',
color: {
......@@ -170,6 +176,7 @@ export const defaultConfig: IConfig = {
shape: 'circle',
type: 'default node type',
},
connectorNode: connectorNodeGroup,
foundDrug: {
groupName: 'Drugs',
color: {
......
src/index.html
+ 1
− 1
View file @ d5a83f31
......@@ -93,7 +93,7 @@
<drugst-one id="netexp1"
pluginId="2"
config='{"identifier":"symbol","licencedDatasets": false, "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":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#ffffff","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":true,"showLegend":true}'
network='{"nodes":[{"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}],"edges":[]}'>
network='{"nodes":[{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"FOXP2","label":"FOXP2","group":"gene"},{"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}],"edges":[]}'>
</drugst-one>
<!-- ENSEMBL test-->
<!-- <drugst-one id="netexp1"-->
......
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