From 10ecc4cbd110269b87f9b37e34324621cbadfbad Mon Sep 17 00:00:00 2001 From: Hrishikesh Paul Date: Wed, 5 Aug 2020 15:20:27 -0400 Subject: [PATCH] updated data and lint --- src/app/indent/indent.component.ts | 10 +++---- src/app/loading/loading.component.html | 1 - src/app/services/bimodal.service.ts | 4 +-- src/app/services/sheet.service.ts | 2 +- src/app/tree/tree.component.ts | 4 +-- src/app/vis/vis.component.ts | 1 - src/assets/data/li.csv | 36 +++++++++++++------------- src/assets/data/liver.csv | 2 +- src/assets/data/lymph.csv | 6 ++--- src/assets/data/si.csv | 2 +- src/assets/data/skin.csv | 14 +++++----- 11 files changed, 39 insertions(+), 43 deletions(-) diff --git a/src/app/indent/indent.component.ts b/src/app/indent/indent.component.ts index 4ec44714..76cfb2ff 100644 --- a/src/app/indent/indent.component.ts +++ b/src/app/indent/indent.component.ts @@ -68,7 +68,7 @@ export class IndentComponent implements OnInit, OnChanges { uberon: node.uberon, level, }; - }; + } ngOnInit(): void { this.indent.setCurrentSheet(this.currentSheet); @@ -103,7 +103,7 @@ export class IndentComponent implements OnInit, OnChanges { } - + async getData() { try { const data = await this.sheet.getSheetData(this.currentSheet); @@ -111,18 +111,18 @@ export class IndentComponent implements OnInit, OnChanges { this.dataSource.data = [this.indent.makeIndentData(this.sheetData.data)]; this.indentTree.treeControl.expandAll(); - this.returnRefresh.emit({ + this.returnRefresh.emit({ comp: 'Indented List', msg: this.sheetData.msg, status: this.sheetData.status, val: true, }); - this.report.reportLog( + this.report.reportLog( `Indented List for ${this.currentSheet.display} successfully rendered.`, 'success', 'msg' ); - + } catch (err) { console.log(err); this.returnRefresh.emit({ diff --git a/src/app/loading/loading.component.html b/src/app/loading/loading.component.html index ee8115a0..6ce248ec 100644 --- a/src/app/loading/loading.component.html +++ b/src/app/loading/loading.component.html @@ -10,7 +10,6 @@ >

Please wait while the data loads...

-

Fetching {{loadingText}} data

diff --git a/src/app/services/bimodal.service.ts b/src/app/services/bimodal.service.ts index 9dbd0784..0ac4bfaa 100644 --- a/src/app/services/bimodal.service.ts +++ b/src/app/services/bimodal.service.ts @@ -80,7 +80,7 @@ export interface ASCTD { export class BimodalService { constructor(public sheet: SheetService, public report: ReportService) { } - + async makeASCTData(sheetData, treeData, bimodalConfig, currentSheet) { let ASCTGraphData: ASCTD; const links = []; @@ -90,7 +90,7 @@ export class BimodalService { const distance = currentSheet.config.bimodal_distance; let id = 0; let biomarkers = []; - + // making anatomical structures (last layer of the tree) treeData.forEach(td => { if (td.children === 0) { diff --git a/src/app/services/sheet.service.ts b/src/app/services/sheet.service.ts index ece398ef..280b4351 100644 --- a/src/app/services/sheet.service.ts +++ b/src/app/services/sheet.service.ts @@ -77,7 +77,7 @@ export class SheetService { public async getDataFromURL(url: string, header_count = 11): Promise { return new Promise(async (res, rej) => { try { - let data = await this.http + const data = await this.http .get(url, { responseType: 'text' }) .toPromise(); const parsedData = parse(data); diff --git a/src/app/tree/tree.component.ts b/src/app/tree/tree.component.ts index 13feae11..c10ceb7b 100644 --- a/src/app/tree/tree.component.ts +++ b/src/app/tree/tree.component.ts @@ -65,9 +65,7 @@ export class TreeComponent implements OnInit, OnChanges, OnDestroy { } }; - constructor(public sheet: SheetService, public report: ReportService, public ts: TreeService, public bms: BimodalService) { - - } + constructor(public sheet: SheetService, public report: ReportService, public ts: TreeService, public bms: BimodalService) { } ngOnInit(): void { diff --git a/src/app/vis/vis.component.ts b/src/app/vis/vis.component.ts index 79360fde..7c6f377c 100644 --- a/src/app/vis/vis.component.ts +++ b/src/app/vis/vis.component.ts @@ -53,7 +53,6 @@ export class VisComponent implements OnInit { this.openLoading(); this.displayGraph = val; this.shouldRefreshData = true; - } refreshData(val) { diff --git a/src/assets/data/li.csv b/src/assets/data/li.csv index dd51cc0d..ae185d9e 100644 --- a/src/assets/data/li.csv +++ b/src/assets/data/li.csv @@ -36,18 +36,18 @@ large bowel,ileo-cecal valve,mucosa,Lamina propria/Gut associated lymphoid tissu large bowel,ileo-cecal valve,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,ileo-cecal valve,mucosa,muscularis mucosa,muscle,aSMA, large bowel,ileo-cecal valve,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,ileo-cecal valve,submucosa,submucosa,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,ileo-cecal valve,submucosa,submucosa,endothelial cell ,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,ileo-cecal valve,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,ileo-cecal valve,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,ileo-cecal valve,submucosa,submucosal plexus of Meissner,muscle,aSMA, large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,muscle,aSMA, large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,Interstitial cell of Cajal,"CD117, CD34", large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" -large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,endothelial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,ileo-cecal valve,muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", large bowel,ileo-cecal valve,muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", large bowel,ileo-cecal valve,muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -large bowel,ileo-cecal valve,serosa,,mesothelial,Cytokeratin, +large bowel,ileo-cecal valve,serosa,,mesothelial cell,Cytokeratin, large bowel,ileo-cecal valve,serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" large bowel,ileo-cecal valve,serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" large bowel,ceacum,mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" @@ -57,7 +57,7 @@ large bowel,ceacum,mucosa,Epithelium,absorptive,,"CA2, SI" large bowel,ceacum,mucosa,Epithelium,goblet,,"MUC2, ITLN1, SLC26A2, CLCA4" large bowel,ceacum,mucosa,Epithelium,enterocyte,,"BEST4, CA7, NEURL1, HES1" large bowel,ceacum,mucosa,Epithelium,Tuft cell,,"DCLK1, IRF7, SELENBP1" -large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial,"CD31, CD34, CD36","CD36, SOX17" +large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial cell,"CD31, CD34, CD36","CD36, SOX17" large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),lymphatics,"CD31, Podoplanin", large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),myofibroblast,,"TP53I3, DES, ACTG2, CNN1" large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" @@ -77,18 +77,18 @@ large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),D large bowel,ceacum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,ceacum,mucosa,muscularis mucosa,muscle,aSMA, large bowel,ceacum,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,ceacum,submucosa,submucosa,endoethlial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,ceacum,submucosa,submucosa,endoethlial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,ceacum,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,ceacum,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,ceacum,submucosa,submucosal plexus of Meissner,muscle,aSMA, large bowel,ceacum,muscularis externa,circular/longitudinal muscle,muscle,aSMA, large bowel,ceacum,muscularis externa,circular/longitudinal muscle,Interstitial cell of Cajal,"CD117, CD34", large bowel,ceacum,muscularis externa,circular/longitudinal muscle,fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" -large bowel,ceacum,muscularis externa,circular/longitudinal muscle,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,ceacum,muscularis externa,circular/longitudinal muscle,endothelial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,ceacum,muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", large bowel,ceacum,muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", large bowel,ceacum,muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -large bowel,ceacum,serosa,,mesothelial,Cytokeratin, +large bowel,ceacum,serosa,,mesothelial cell,Cytokeratin, large bowel,ceacum,serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" large bowel,ceacum,serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" large bowel,Appendix,mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" @@ -98,7 +98,7 @@ large bowel,Appendix,mucosa,Epithelium,absorptive,,"CA2, SI" large bowel,Appendix,mucosa,Epithelium,goblet,,"MUC2, ITLN1, SLC26A2, CLCA4" large bowel,Appendix,mucosa,Epithelium,enterocyte,,"BEST4, CA7, NEURL1, HES1" large bowel,Appendix,mucosa,Epithelium,Tuft cell,,"DCLK1, IRF7, SELENBP1" -large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial,"CD31, CD34, CD36","CD36, SOX17" +large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial cell,"CD31, CD34, CD36","CD36, SOX17" large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),lymphatics,"CD31, Podoplanin", large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),myofibroblast,,"TP53I3, DES, ACTG2, CNN1" large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" @@ -118,18 +118,18 @@ large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT) large bowel,Appendix,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,Appendix,mucosa,muscularis mucosa,muscle,aSMA, large bowel,Appendix,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,Appendix,submucosa,submucosa,endoethlial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,Appendix,submucosa,submucosa,endoethlial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,Appendix,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,Appendix,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,Appendix,submucosa,submucosal plexus of Meissner,muscle,aSMA, large bowel,Appendix,muscularis externa,circular/longitudinal muscle,muscle,aSMA, large bowel,Appendix,muscularis externa,circular/longitudinal muscle,Interstitial cell of Cajal,"CD117, CD34", large bowel,Appendix,muscularis externa,circular/longitudinal muscle,fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" -large bowel,Appendix,muscularis externa,circular/longitudinal muscle,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,Appendix,muscularis externa,circular/longitudinal muscle,endothelial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,Appendix,muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", large bowel,Appendix,muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", large bowel,Appendix,muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -large bowel,Appendix,serosa,,mesothelial,Cytokeratin, +large bowel,Appendix,serosa,,mesothelial cell,Cytokeratin, large bowel,Appendix,serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" large bowel,Appendix,serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" large bowel,colon ascending/right,mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" @@ -139,7 +139,7 @@ large bowel,colon ascending/right,mucosa,Epithelium,absorptive,,"CA2, SI" large bowel,colon ascending/right,mucosa,Epithelium,goblet,,"MUC2, ITLN1, SLC26A2, CLCA4" large bowel,colon ascending/right,mucosa,Epithelium,enterocyte,,"BEST4, CA7, NEURL1, HES1" large bowel,colon ascending/right,mucosa,Epithelium,Tuft cell,,"DCLK1, IRF7, SELENBP1" -large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial,"CD31, CD34, CD36","CD36, SOX17" +large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),endothelial cell,"CD31, CD34, CD36","CD36, SOX17" large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),lymphatics,"CD31, Podoplanin", large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),myofibroblast,,"TP53I3, DES, ACTG2, CNN1" large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" @@ -159,18 +159,18 @@ large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid large bowel,colon ascending/right,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,colon ascending/right,mucosa,muscularis mucosa,muscle,aSMA, large bowel,colon ascending/right,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,colon ascending/right,submucosa,submucosa,endoethlial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,colon ascending/right,submucosa,submucosa,endoethlial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,colon ascending/right,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,colon ascending/right,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,colon ascending/right,submucosa,submucosal plexus of Meissner,muscle,aSMA, large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,muscle,aSMA, large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,Interstitial cell of Cajal,"CD117, CD34", large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,fibroblast,"Col6A1, Col6A2","COL6A1, COL6A2" -large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,endothelial cell,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,colon ascending/right,muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", large bowel,colon ascending/right,muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", large bowel,colon ascending/right,muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -large bowel,colon ascending/right,serosa,,mesothelial,Cytokeratin, +large bowel,colon ascending/right,serosa,,mesothelial cell,Cytokeratin, large bowel,colon ascending/right,serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" large bowel,colon ascending/right,serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" large bowel,"colon, transverse",mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" @@ -323,7 +323,7 @@ large bowel,rectum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),D large bowel,rectum,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,rectum,mucosa,muscularis mucosa,muscle,aSMA, large bowel,rectum,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,rectum,submucosa,submucosa,endoethlial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,rectum,submucosa,submucosa,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,rectum,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,rectum,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,rectum,submucosa,submucosal plexus of Meissner,muscle,aSMA, @@ -334,7 +334,7 @@ large bowel,rectum,muscularis externa,circular/longitudinal muscle,endothelial," large bowel,rectum,muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", large bowel,rectum,muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", large bowel,rectum,muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -large bowel,rectum,serosa,,mesothelial,Cytokeratin, +large bowel,rectum,serosa,,mesothelial cell,Cytokeratin, large bowel,rectum,serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" large bowel,rectum,serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" large bowel,anal canal,mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" @@ -364,7 +364,7 @@ large bowel,anal canal,mucosa,Lamina propria/Gut associated lymphoid tissue (GAL large bowel,anal canal,mucosa,Lamina propria/Gut associated lymphoid tissue (GALT),Innate lymphoid cell,"CD127, CD117, CD161", large bowel,anal canal,mucosa,muscularis mucosa,muscle,aSMA, large bowel,anal canal,submucosa,submucosa,nerve,"PDL1, CD56, PGP9.5", -large bowel,anal canal,submucosa,submucosa,endoethlial,"CD31, CD34, CD36","NOVA2, SOX17" +large bowel,anal canal,submucosa,submucosa,endothelial,"CD31, CD34, CD36","NOVA2, SOX17" large bowel,anal canal,submucosa,submucosa,lymphatic,"CD31, Podoplanin", large bowel,anal canal,submucosa,submucosal plexus of Meissner,nerve,"PDL1, CD56, PGP9.5", large bowel,anal canal,submucosa,submucosal plexus of Meissner,muscle,aSMA, diff --git a/src/assets/data/liver.csv b/src/assets/data/liver.csv index 217e714c..cd61214c 100644 --- a/src/assets/data/liver.csv +++ b/src/assets/data/liver.csv @@ -33,7 +33,7 @@ hepatic Lobule,Liver immune resident component,,conventional Dendritic cell,,"CD hepatic Lobule,Liver immune resident component,,Conventional DC 1,,CD141+ (BDCA-3) hepatic Lobule,Liver immune resident component,,Conventional DC 2,,CD1c (BDCA-1) hepatic Lobule,Liver immune resident component,,plasmacytoid Dendritic cell,,CD11c Neg -hepatic Lobule,Liver immune resident component,,CD8 TRm (residence memory),HOBIT and BLIMP1,"CD8, TCRαβ, CD69 and CD103" +hepatic Lobule,Liver immune resident component,,CD8 TRm (residence memory),"HOBIT, BLIMP1","CD8, TCRαβ, CD69 and CD103" hepatic Lobule,Liver immune resident component,,CD4+T cell,,"CD4, TCRαβ" hepatic Lobule,Liver immune resident component,,gamma delta T cell,,"γδTCR,CD27lo, CD45RAlo subset of Vδ1+ T, CD69, CXCR3, and CXCR6" hepatic Lobule,Liver immune resident component,,CD8+ Liver-Resident Memory T cell,,"CXCR3 and CXCR6, CCR7, CD62L, KLF2, and S1PR1" diff --git a/src/assets/data/lymph.csv b/src/assets/data/lymph.csv index fe4f6078..90255320 100644 --- a/src/assets/data/lymph.csv +++ b/src/assets/data/lymph.csv @@ -23,11 +23,11 @@ Lobule,Trabecular Sinus,,,Neutrophil,MPO+ Lobule,Venule,Blood Vessels,,Blood Endothelial Cell,"CD31+, CD34+, CD105+" Lobule,Arteriole,Blood Vessels,,Blood Endothelial Cell,"CD31+, CD34+, CD105+" Lobule,Primary Follicle,,,Follicular Dendritic Cell,"CD21+, CD35+" -Lobule,Primary Follicle,,,Naive B Cell,"CD45RA+, CD21+, CD20+, IgM+, IgD+, CD23+,HLA DR+" +Lobule,Primary Follicle,,,Naive B Cell,"CD45RA+, CD21+, CD20+, IgM+, IgD+, CD23+,HLA-DR+" Lobule,Primary Follicle,,,Mature B Cell,"CD19+, CD20+, CD79a+,CD45RO+" Lobule,Primary Follicle,,,Macrophage,"CD11b+, CD169+" Lobule,Primary Follicle,,,Fibroblastic Reticular Cell,"Podoplanin+, Desmin+, Collagen I+, Smooth Muscle Actin+" -Lobule,Secondary Follicle,Germinal Center,Light Zone,Follicular Dendritic Cell,"HLA DR+, Podoplanin+, CD21+, CD23+, CD35+" +Lobule,Secondary Follicle,Germinal Center,Light Zone,Follicular Dendritic Cell,"HLA-DR+, Podoplanin+, CD21+, CD23+, CD35+" Lobule,Secondary Follicle,Germinal Center,Light Zone,Centrocytes,"CD21+, CD10+, Ki67+, CXCR5+" Lobule,Secondary Follicle,Germinal Center,Light Zone,T Follicular Helper cell,"CD4+, CXCR5+, CD69+, CD10+, PD-1+" Lobule,Secondary Follicle,Germinal Center,Light Zone,T follicular regulatory helper ,"CD4+, FOXP3+, PD-1+" @@ -35,7 +35,7 @@ Lobule,Secondary Follicle,Germinal Center,Light Zone,Tingible Body Macrophage,"C Lobule,Secondary Follicle,Germinal Center,Light Zone,Plasmablast,"CD138+, CD79a+" Lobule,Secondary Follicle,Germinal Center,Dark Zone,Centroblast,"CXCR4+, HLA-DR+, CD10+, CD19+" Lobule,Secondary Follicle,Germinal Center,Dark Zone,Reticular cell,"CXCL12+, Collagen IV+, Laminin+" -Lobule,Secondary Follicle,Germinal Center,Mantle Zone,Naive B cell,"HLA DR+, IgM+, IgD+, CD20+, CD19+, CD45RA+, CD79a+, CD21+" +Lobule,Secondary Follicle,Germinal Center,Mantle Zone,Naive B cell,"HLA-DR+, IgM+, IgD+, CD20+, CD19+, CD45RA+, CD79a+, CD21+" Lobule,Secondary Follicle,Germinal Center,Mantle Zone,Macrophage,"CD169+, CD11b+" Lobule,Secondary Follicle,Germinal Center,Mantle Zone,Memory B cell,"CD45+, CD20+, CD19+" Lobule,Secondary Follicle,Germinal Center,Mantle Zone,T Helper cell,"CD3+, CD4+" diff --git a/src/assets/data/si.csv b/src/assets/data/si.csv index 85d683b8..ab2723d2 100644 --- a/src/assets/data/si.csv +++ b/src/assets/data/si.csv @@ -88,7 +88,7 @@ Small bowel,"duodenum, descending",muscularis externa,circular/longitudinal musc Small bowel,"duodenum, descending",muscularis externa,circular/longitudinal muscle,nerve,"PDL1, CD56, PGP9.5", Small bowel,"duodenum, descending",muscularis externa,myenteric plexus of Auerbach,nerve,"PDL1, CD56, PGP9.5", Small bowel,"duodenum, descending",muscularis externa,myenteric plexus of Auerbach,muscle,aSMA, -Small bowel,"duodenum, descending",serosa,,mesothelial,Cytokeratin, +Small bowel,"duodenum, descending",serosa,,mesothelial cell,Cytokeratin, Small bowel,"duodenum, descending",serosa,connective tissue,fibroblast,,"COL6A1, COL6A2" Small bowel,"duodenum, descending",serosa,connective tissue,endothelial cell,,"NOVA2, SOX17" Small bowel,"duodenum, horizontal",mucosa,Epithelium,epithelial stem cell,"CD34, SOX9, CD44","LGR5, ASCL2, CDHR1, BIRC3, MYL9" diff --git a/src/assets/data/skin.csv b/src/assets/data/skin.csv index 6b9da1b6..54565284 100644 --- a/src/assets/data/skin.csv +++ b/src/assets/data/skin.csv @@ -10,20 +10,20 @@ flattened table verified and formatting adjusted to match ASCT-B reporter requir ,,,, //Main Layers,//Sub Layers,//Other structures,//Major cell types,//Markers Epidermis,Stratum corneum (SC),,Corneocyte,"Involucrin, Fillagrin" -Epidermis,Stratum granulosum (SG),,Keratinocyte,"Specific keratins (k2/k10); P63, p40; panCK (PCK26, AE1)" +Epidermis,Stratum granulosum (SG),,Keratinocyte,"Keratin k2, Keratin k10; P63, p40, panCK (PCK26, AE1)" Epidermis,Stratum granulosum (SG),,Langerhans cell,"CD1a, Langerin" -Epidermis,Stratum spinosum (SS),,Keratinocytes,"Specific keratins (k1/k10); P63, p40; panCK (PCK26, AE1)" +Epidermis,Stratum spinosum (SS),,Keratinocytes,"keratin k1, keratin k10, P63, p40, panCK (PCK26, AE1)" Epidermis,Stratum spinosum (SS),,Langerhans cell,"CD1a, Langerin" Epidermis,Stratum spinosum (SS),,Merkel cell,"Synaptophysin, chromogranin, CK20, neuron specific enolase" -Epidermis,Stratum basale (SB),,Keratinocyte,"Specific keratins (k5/k14); P63, p40; panCK (PCK26, AE1)" +Epidermis,Stratum basale (SB),,Keratinocyte,"keratin k5, keratin k14, P63, p40, panCK (PCK26, AE1)" Epidermis,Stratum basale (SB),,Langerhans cell,"CD1a, Langerin" Epidermis,Stratum basale (SB),,Merkel cell,"Synaptophysin, chromogranin, CK20, neuron specific enolase" Epidermis,Stratum basale (SB),,Melanocyte,"SOX-10, S100, MelanA" Epidermis,,Nail plate,Onychocyte,"Keratins, panCK (PCK26, AE1)" Epidermis,,Hair follicles,Dead and live keratinocyte,"Keratins, panCK (PCK26, AE1)" Epidermis,,Sebaceous glands,"Germinative (epithelial) cell, Sebocyte","EMA, adipophilin, peripilin, panCK (PCK26, AE1)" -Epidermis,,Eccrine (sweat) glands,"Eccrine cell, myoepithelial cell","Keratins and S100, panCK (PCK26, AE1)" -Epidermis,,Apocrine glands,"Apocrine cell, myoepithelial cell","Keratins and GCDFP, GATA3" +Epidermis,,Eccrine (sweat) glands,"Eccrine cell, myoepithelial cell","Keratin, S100, panCK (PCK26, AE1)" +Epidermis,,Apocrine glands,"Apocrine cell, myoepithelial cell","Keratin, GCDFP, GATA3" Dermis,,,Myoepithelial cell,"SMA, calponin, S100, p63, p40" Dermis,,,Fibroblast,"Factor XIIIa, Vimentin, CD34" Dermis,,,Mast cell,"CD203c, c-Kit (CD117)" @@ -35,14 +35,14 @@ Dermis,,,T reg,"CD3, CD4, FOXP3" Dermis,,,B cell,"CD19, CD20, CD79a" Dermis,,,Neutrophil,"MPO, CD43" Dermis,,,Eosinophil,"CD9, MPO" -Dermis,,nerve,Axons,"NFP1, PGP9.5" +Dermis,,nerve,Axon,"NFP1, PGP9.5" Dermis,,,Schwann cell,S100 Dermis,,,Perineurial cell,"EMA, CD34" Dermis,,Blood vessels,Endothelial cell,"CD31, ERG" Dermis,,,Perivascular smooth muscle cell,"SMA, calponin, h-caldesmon" Dermis,,,Glomus cell,"SMA, calponin, h-caldesmon" Dermis,,,Pericyte,SMA -Dermis,,,Lymphatic,"D2-40 (podoplanin), LYVE1" +Dermis,,,Lymphatic,"D2-40 (podoplanin), LYVE-1" Subcutaneous,,,Adipocyte,"S100, calretinin" Subcutaneous,,,Fibroblast,"Factor XIIIa, Vimentin, CD34" Subcutaneous,,,Macrophage,"CD68, CD163"