diff --git a/package-lock.json b/package-lock.json index 17f8c605798c2c11b9b97e0a36015bcbd8ab1703..279dcf9a58246cda1a1d811af556d7a7ba6cd519 100644 --- a/package-lock.json +++ b/package-lock.json @@ -29753,7 +29753,7 @@ "fs.realpath": "^1.0.0", "inflight": "^1.0.4", "inherits": "2", - "minimatch": "~3.0.5", + "minimatch": "^3.1.1", "once": "^1.3.0", "path-is-absolute": "^1.0.0" } @@ -30080,7 +30080,7 @@ "fs.realpath": "^1.0.0", "inflight": "^1.0.4", "inherits": "2", - "minimatch": "~3.0.5", + "minimatch": "^3.1.1", "once": "^1.3.0", "path-is-absolute": "^1.0.0" } diff --git a/src/app/pages/explorer-page/explorer-page.component.scss b/src/app/pages/explorer-page/explorer-page.component.scss index 1464f1993b22e29c1414c1d8b6600d21346d6076..817eff9536987064fda0c8f68042584ab3d34144 100644 --- a/src/app/pages/explorer-page/explorer-page.component.scss +++ b/src/app/pages/explorer-page/explorer-page.component.scss @@ -8,7 +8,7 @@ } .seed-selection { - max-height: 600px; + max-height: 800px; } .quick-find { diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts index fd8b8051cd93094d22e812be0f78c20cd65987ff..b631e2e49861d23ba2fab6b751de0c61205d12f2 100644 --- a/src/app/services/analysis/analysis.service.ts +++ b/src/app/services/analysis/analysis.service.ts @@ -224,7 +224,7 @@ export class AnalysisService { } }); const selectedNodes = new Set(this.selectedItems.keys()); - const firstNeighborNodes: Set<string> = new Set(); + const firstNeighborNodes: Set<string> = new Set(selectedNodes); this.networkHandler.activeNetwork.currentViewEdges.forEach(edge => { if (selectedNodes.has(edge.from)) { firstNeighborNodes.add(edge.to); @@ -235,13 +235,15 @@ export class AnalysisService { }); firstNeighborNodes.forEach(n => { - wrappers.push(getWrapperFromNode(mappedNodes[n])); + if (mappedNodes[n]) { + wrappers.push(getWrapperFromNode(mappedNodes[n])); + } }); this.addItems(wrappers); } - public rectangleSelect(){ + public rectangleSelect() { this.networkHandler.activeNetwork.rectangleSelect(true); } @@ -269,8 +271,10 @@ export class AnalysisService { } selectedNodes.forEach(n => { - if (!this.selectedItems.has(n)){ - wrappers.push(getWrapperFromNode(mappedNodes[n])); + if (!this.selectedItems.has(n)) { + if (mappedNodes[n]) { + wrappers.push(getWrapperFromNode(mappedNodes[n])); + } } }); this.addItems(wrappers); diff --git a/src/index.html b/src/index.html index d4703eb1f552a30d22b7693fed985adeb37ec51c..dbef3b20d384fe9e678453147d9257b37a2f9d28 100644 --- a/src/index.html +++ b/src/index.html @@ -114,38 +114,9 @@ menu<br> <!-- task-id="ks38WxeCSdbXk2cajKACinnUnCHWbf4I" --> <drugst-one id="netexp1" - config='{"activateNetworkMenuButtonAdjacentDisorders":false,"activateNetworkMenuButtonAdjacentDrugs":false, "activateNetworkMenuButtonAdjacentDisordersDrugs": false, "licensedDatasets":true}' - groups='{"nodeGroups":{"protein":{"type":"protein","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Protein","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}' - network='{"nodes":[{ "id": "ATG16L1", "group": "protein", "label": "ATG16L1" }, - { "id": "ICAM1", "group": "protein", "label": "ICAM1" }, - { "id": "TNF", "group": "protein", "label": "TNF" }, - { "id": "SFRP2", "group": "protein", "label": "SFRP2" }, - { "id": "APC2", "group": "protein", "label": "APC2" }, - { "id": "IL10", "group": "protein", "label": "IL10" }, - { "id": "CUL2", "group": "protein", "label": "CUL2" }, - { "id": "SFRP1", "group": "protein", "label": "SFRP1" }, - { "id": "TNFSF15", "group": "protein", "label": "TNFSF15" }, - { "id": "ITGA4", "group": "protein", "label": "ITGA4" }, - { "id": "DEFA5", "group": "protein", "label": "DEFA5" }, - { "id": "MUC19", "group": "protein", "label": "MUC19" }, - { "id": "SLAMF8", "group": "protein", "label": "SLAMF8" }, - { "id": "APC", "group": "protein", "label": "APC" }, - { "id": "IL6", "group": "protein", "label": "IL6" }, - { "id": "INAVA", "group": "protein", "label": "INAVA" }, - { "id": "CARD9", "group": "protein", "label": "CARD9" }, - { "id": "ITGB8", "group": "protein", "label": "ITGB8" }, - { "id": "IL23R", "group": "protein", "label": "IL23R" }, - { "id": "NOD2", "group": "protein", "label": "NOD2" }, - { "id": "RASSF1", "group": "protein", "label": "RASSF1" }, - { "id": "SLC11A1", "group": "protein", "label": "SLC11A1" }, - { "id": "IL18RAP", "group": "protein", "label": "IL18RAP" }, - { "id": "TGFB1", "group": "protein", "label": "TGFB1" }, - { "id": "IRGM", "group": "protein", "label": "IRGM" }, - { "id": "PLCG2", "group": "protein", "label": "PLCG2" }, - { "id": "PTPN22", "group": "protein", "label": "PTPN22" }, - { "id": "PTGS2", "group": "protein", "label": "PTGS2" }, - { "id": "VNN1", "group": "protein", "label": "VNN1" }, - { "id": "ITGAL", "group": "protein", "label": "ITGAL" }]}'> + groups='{"nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Seed","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Discovered target","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}' + config='{"customEdges":{"default":true, "selectable":false}, "showAdvAnalysisContent":["drug-search", "enrichment-gprofiler", "enrichment-digest", "search-ndex"],"identifier":"symbol","title":"ROBUST output network", "taskDrugName": "Drug Search", "showLegendNodes": true, "showLegendEdges": true, "showSidebar": "left", "showOverview": true, "legendPos": "left", "legendClass": "legend", "showQuery": true, "showItemSelector": true,"showSimpleAnalysis": false,"showAdvAnalysis": true,"showSelection": true,"showTasks": true,"showNetworkMenu": "right","showLegend": true,"showNetworkMenuButtonExpression": true, "showNetworkMenuButtonScreenshot": true,"showNetworkMenuButtonExportGraphml": true,"showNetworkMenuButtonAdjacentDrugs": true,"showNetworkMenuButtonCenter": true,"showConnectGenes": false,"networkMenuButtonAdjacentDrugsLabel": "Drugs","showNetworkMenuButtonAdjacentDisordersProteins": true,"networkMenuButtonAdjacentDisordersProteinsLabel": "Disorders (protein)","showNetworkMenuButtonAdjacentDisordersDrugs": true,"networkMenuButtonAdjacentDisordersDrugsLabel": "Disorders (drug)","showNetworkMenuButtonAnimation": true,"networkMenuButtonAnimationLabel": "Animation", "autofillEdges": false, "physicsOn": false,"useNedrexLicenced": true,"selfReferences": false, "interactionDrugProtein": "NeDRex", "indicationDrugDisorder": "NeDRex","nodeShadow": true,"edgeShadow": true, "algorithms": {"drug": ["trustrank", "closeness", "degree", "proximity"], "drug-target": ["trustrank", "multisteiner", "keypathwayminer", "degree", "closeness", "betweenness"]}, "associatedProteinDisorder": "NeDRex", "nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Seed","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Discovered target","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}' + network='{"nodes": [{"id": "DEFA1", "group": "gene"}, {"id": "CST6", "group": "gene"}, {"id": "IGFBP2", "group": "gene"}, {"id": "TNFSF8", "group": "gene"}, {"id": "COPRS", "group": "gene"}, {"id": "AGT", "group": "important"}, {"id": "IL6", "group": "important"}, {"id": "A2M", "group": "gene"}, {"id": "NLRP3", "group": "important"}, {"id": "TLR4", "group": "important"}, {"id": "TNFSF9", "group": "gene"}, {"id": "RPL18", "group": "gene"}, {"id": "F5", "group": "gene"}, {"id": "IVL", "group": "gene"}, {"id": "IL6R", "group": "gene"}, {"id": "CPB2", "group": "gene"}, {"id": "CCDC8", "group": "gene"}, {"id": "SERPINB6", "group": "gene"}, {"id": "MBL2", "group": "important"}, {"id": "IL1B", "group": "important"}, {"id": "HIST1H3E", "group": "gene"}, {"id": "IL24", "group": "gene"}, {"id": "GSDMB", "group": "gene"}, {"id": "NOTCH2", "group": "gene"}, {"id": "F2", "group": "important"}, {"id": "CCR5", "group": "important"}, {"id": "SERPINB8", "group": "gene"}, {"id": "KRT1", "group": "gene"}, {"id": "IL1RN", "group": "important"}, {"id": "PLAT", "group": "gene"}, {"id": "URB1", "group": "gene"}, {"id": "FCF1", "group": "gene"}, {"id": "ACE", "group": "important"}, {"id": "THBS3", "group": "gene"}, {"id": "CALML3", "group": "gene"}, {"id": "PSMA5", "group": "gene"}, {"id": "NDUFA3", "group": "gene"}, {"id": "PARK2", "group": "gene"}, {"id": "FANCB", "group": "gene"}, {"id": "SERPINB2", "group": "gene"}, {"id": "KLRG2", "group": "gene"}, {"id": "FAM19A3", "group": "gene"}, {"id": "CRYZL1", "group": "gene"}, {"id": "HEATR1", "group": "gene"}, {"id": "IGHG2", "group": "gene"}, {"id": "C17orf70", "group": "gene"}, {"id": "TINAG", "group": "gene"}, {"id": "RSPRY1", "group": "gene"}, {"id": "TMPRSS11A", "group": "gene"}, {"id": "SLC18A1", "group": "gene"}, {"id": "PSMD1", "group": "gene"}, {"id": "PCDHB15", "group": "gene"}, {"id": "TSR3", "group": "gene"}, {"id": "FGL1", "group": "gene"}, {"id": "C7orf60", "group": "gene"}, {"id": "SSR3", "group": "gene"}, {"id": "REN", "group": "gene"}, {"id": "MYH14", "group": "gene"}, {"id": "TBCK", "group": "gene"}, {"id": "DARS", "group": "gene"}, {"id": "C16orf70", "group": "gene"}, {"id": "DQX1", "group": "gene"}, {"id": "RPL30", "group": "gene"}, {"id": "FBXO30", "group": "gene"}, {"id": "EPPK1", "group": "gene"}, {"id": "LAMA1", "group": "gene"}, {"id": "AP4E1", "group": "gene"}, {"id": "AP4S1", "group": "gene"}, {"id": "HIST1H1B", "group": "gene"}, {"id": "AFP", "group": "gene"}], "edges": [{"from": "DEFA1", "to": "PLAT", "group": "default"}, {"from": "DEFA1", "to": "IGFBP2", "group": "default"}, {"from": "CST6", "to": "FCF1", "group": "default"}, {"from": "CST6", "to": "NOTCH2", "group": "default"}, {"from": "IGFBP2", "to": "GSDMB", "group": "default"}, {"from": "TNFSF8", "to": "F5", "group": "default"}, {"from": "TNFSF8", "to": "TNFSF9", "group": "default"}, {"from": "COPRS", "to": "HIST1H3E", "group": "default"}, {"from": "COPRS", "to": "IL6R", "group": "default"}, {"from": "AGT", "to": "ACE", "group": "default"}, {"from": "AGT", "to": "GSDMB", "group": "default"}, {"from": "AGT", "to": "NDUFA3", "group": "default"}, {"from": "AGT", "to": "REN", "group": "default"}, {"from": "IL6", "to": "IL6R", "group": "default"}, {"from": "A2M", "to": "IL1B", "group": "default"}, {"from": "A2M", "to": "CPB2", "group": "default"}, {"from": "NLRP3", "to": "URB1", "group": "default"}, {"from": "NLRP3", "to": "HIST1H1B", "group": "default"}, {"from": "TLR4", "to": "TNFSF9", "group": "default"}, {"from": "TNFSF9", "to": "KLRG2", "group": "default"}, {"from": "RPL18", "to": "FCF1", "group": "default"}, {"from": "RPL18", "to": "URB1", "group": "default"}, {"from": "F5", "to": "F2", "group": "default"}, {"from": "F5", "to": "CCDC8", "group": "default"}, {"from": "F5", "to": "KLRG2", "group": "default"}, {"from": "IVL", "to": "FCF1", "group": "default"}, {"from": "IVL", "to": "KRT1", "group": "default"}, {"from": "IL6R", "to": "FANCB", "group": "default"}, {"from": "IL6R", "to": "CRYZL1", "group": "default"}, {"from": "IL6R", "to": "C17orf70", "group": "default"}, {"from": "IL6R", "to": "TBCK", "group": "default"}, {"from": "CPB2", "to": "F2", "group": "default"}, {"from": "CPB2", "to": "TINAG", "group": "default"}, {"from": "CCDC8", "to": "HEATR1", "group": "default"}, {"from": "CCDC8", "to": "PSMD1", "group": "default"}, {"from": "CCDC8", "to": "DARS", "group": "default"}, {"from": "SERPINB6", "to": "F2", "group": "default"}, {"from": "SERPINB6", "to": "SERPINB8", "group": "default"}, {"from": "SERPINB6", "to": "TMPRSS11A", "group": "default"}, {"from": "SERPINB6", "to": "C16orf70", "group": "default"}, {"from": "MBL2", "to": "KRT1", "group": "default"}, {"from": "IL24", "to": "NOTCH2", "group": "default"}, {"from": "IL24", "to": "CCR5", "group": "default"}, {"from": "F2", "to": "PLAT", "group": "default"}, {"from": "CCR5", "to": "PSMA5", "group": "default"}, {"from": "CCR5", "to": "AFP", "group": "default"}, {"from": "SERPINB8", "to": "FCF1", "group": "default"}, {"from": "IL1RN", "to": "FCF1", "group": "default"}, {"from": "PLAT", "to": "SERPINB2", "group": "default"}, {"from": "PLAT", "to": "FGL1", "group": "default"}, {"from": "PLAT", "to": "LAMA1", "group": "default"}, {"from": "FCF1", "to": "CALML3", "group": "default"}, {"from": "FCF1", "to": "SERPINB2", "group": "default"}, {"from": "FCF1", "to": "IGHG2", "group": "default"}, {"from": "FCF1", "to": "MYH14", "group": "default"}, {"from": "FCF1", "to": "RPL30", "group": "default"}, {"from": "FCF1", "to": "EPPK1", "group": "default"}, {"from": "THBS3", "to": "NDUFA3", "group": "default"}, {"from": "THBS3", "to": "FANCB", "group": "default"}, {"from": "CALML3", "to": "PARK2", "group": "default"}, {"from": "PSMA5", "to": "PARK2", "group": "default"}, {"from": "PSMA5", "to": "HEATR1", "group": "default"}, {"from": "PSMA5", "to": "PSMD1", "group": "default"}, {"from": "PSMA5", "to": "DARS", "group": "default"}, {"from": "NDUFA3", "to": "SLC18A1", "group": "default"}, {"from": "NDUFA3", "to": "DQX1", "group": "default"}, {"from": "FAM19A3", "to": "CRYZL1", "group": "default"}, {"from": "RSPRY1", "to": "TMPRSS11A", "group": "default"}, {"from": "RSPRY1", "to": "SLC18A1", "group": "default"}, {"from": "PCDHB15", "to": "SSR3", "group": "default"}, {"from": "PCDHB15", "to": "TBCK", "group": "default"}, {"from": "TSR3", "to": "FGL1", "group": "default"}, {"from": "TSR3", "to": "C7orf60", "group": "default"}, {"from": "C7orf60", "to": "REN", "group": "default"}, {"from": "SSR3", "to": "MYH14", "group": "default"}, {"from": "C16orf70", "to": "FBXO30", "group": "default"}, {"from": "DQX1", "to": "FBXO30", "group": "default"}, {"from": "LAMA1", "to": "AP4E1", "group": "default"}, {"from": "AP4E1", "to": "AP4S1", "group": "default"}, {"from": "AP4S1", "to": "AFP", "group": "default"}]}'> </drugst-one> diff --git a/src/stylesheets/styles.scss b/src/stylesheets/styles.scss index f3b93dd1aef9077bf45b5b2bfc3aec27510104a8..a43cf533de5d57d7aff80c19e1128b039e5ab801 100644 --- a/src/stylesheets/styles.scss +++ b/src/stylesheets/styles.scss @@ -133,7 +133,7 @@ div.card.bar-large { margin: 5px; - max-height: 600px; + max-height: 800px; } div.card-content.overflow {