From 64f0930c1740411e430bf1a552872954f1ae18a0 Mon Sep 17 00:00:00 2001
From: Michael Hartung <michi@Michaels-MacBook-Pro.local>
Date: Mon, 12 Jul 2021 20:32:48 +0200
Subject: [PATCH] fix analysis network default style
---
.../analysis-panel.component.ts | 24 ++++++++-----------
src/app/interfaces.ts | 11 +++++----
2 files changed, 16 insertions(+), 19 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 58746d63..a62795cf 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -18,9 +18,9 @@ import {
getNodeIdsFromPDI,
getNodeIdsFromPPI,
getProteinNodeId,
- getWrapperFromCustom,
getWrapperFromDrug,
getWrapperFromNode,
+ getWrapperFromProtein,
Node,
Task,
Tissue,
@@ -214,7 +214,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- console.log(node)
if (node.nodeType === 'drug' || node.netexId === undefined || !node.netexId.startsWith('p')) {
return;
}
@@ -391,7 +390,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
* For the third case, fall back to a default case which can also be set by user.
*/
public inferNodeGroup(wrapper: Wrapper): string {
- console.log(wrapper);
if (wrapper.data.group !== undefined) {
return wrapper.data.group;
} else if (wrapper.data.netexId !== undefined && wrapper.data.netexId.startsWith('d')) {
@@ -432,9 +430,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
// add drugGroup and foundNodesGroup for added nodes
// these groups can be overwritten by the user
- console.log("result")
- console.log(result)
-
const nodes = [];
const edges = [];
@@ -451,22 +446,23 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const wrappers: { [key: string]: Wrapper } = {};
for (const node of network.nodes) {
- if (nodeTypes[node] === 'protein') {
+ // convert id to netex Id if exists
+ const nodeDetails = details[node];
+ 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
- this.proteins.push(details[node]);
- wrappers[node] = getWrapperFromNode(details[node]);
- } else if (nodeTypes[node] === 'drug') {
+ this.proteins.push(nodeDetails);
+ wrappers[node] = getWrapperFromProtein(nodeDetails as Node);
+ } else if (nodeDetails.netexId && nodeDetails.netexId.startsWith('d')) {
// node is drug, was found during analysis
- wrappers[node] = getWrapperFromDrug(details[node]);
+ wrappers[node] = getWrapperFromDrug(nodeDetails as Drug);
} else {
// node is custom input from user, could not be mapped to backend protein
- wrappers[node] = getWrapperFromCustom(details[node]);
+ wrappers[node] = getWrapperFromNode(nodeDetails as Node);
}
// IMPORTANT we set seeds to "selected" and not to seeds. The user should be inspired to run
// further analysis and the button function can be used to highlight seeds
- // option to use details[node] as gradient, but sccores are very small
- console.log(details[node])
+ // option to use scores[node] as gradient, but sccores are very small
nodes.push(NetworkSettings.getNodeStyle(wrappers[node].data as Node, config, false, isSeed[node], 1))
}
for (const edge of network.edges) {
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index ac8dee3c..69fcc9a3 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -140,14 +140,15 @@ export function getId(gene: Node) {
return `${gene.id}`;
}
-export function getWrapperFromCustom(gene: Node): Wrapper {
+export function getWrapperFromProtein(gene: Node): Wrapper {
/**
* Constructs wrapper interface for gene
*/
- // if gene.label is undefined, set it to id
+ // if node does not have property group, it was found by the analysis
+ gene.group = gene.group ? gene.group : 'foundNode';
gene.label = gene.label ? gene.label : gene.id
return {
- id: getNodeId(gene),
+ id: getNetworkId(gene),
data: gene,
};
}
@@ -156,8 +157,8 @@ export function getWrapperFromNode(gene: Node): Wrapper {
/**
* Constructs wrapper interface for gene
*/
- // if node does not have property group, it was found by the analysis
- gene.group = gene.group ? gene.group : 'foundNode';
+ // if node does not have property group, it was custom node from user
+ gene.group = gene.group ? gene.group : 'default';
gene.label = gene.label ? gene.label : gene.id
return {
id: getNetworkId(gene),
--
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