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allow custom markerData and cellTypeData
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@thejohnhoffer
thejohnhoffer committed Apr 13, 2021
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10 changes: 8 additions & 2 deletions main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -142,8 +142,8 @@ const arrange_images = function(viewer, tileSources, hashstate, init) {
}
};

const marker_data = [{"String":"ARL13B","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ARL13B&keywords=ARL13B"},{"String":"ASMA","Alias":"A-SMA, a-SMA, alpha-SMA, α-SMA","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ACTA2&keywords=alpha,smooth,muscle,actin"},{"String":"BANF1","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=BANF1&keywords=BANF1"},{"String":"CD11B","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAM&keywords=CD11B"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD14"},{"String":"CD163","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD163&keywords=CD163"},{"String":"CD19","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD19&keywords=CD19"},{"String":"CD20","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MS4A1&keywords=CD20"},{"String":"CD21","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CR2&keywords=CD21"},{"String":"CD3D","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD3D&keywords=CD3D"},{"String":"CD4","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4&keywords=CD4"},{"String":"CD45","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PTPRC&keywords=CD45"},{"String":"CD45RB","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PTPRC&keywords=CD45RB"},{"String":"CD68","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD68&keywords=CD68"},{"String":"CD8A","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8A&keywords=CD8A"},{"String":"FOXP3","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=FOXP3&keywords=FOXP3"},{"String":"GFAP","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=GFAP&keywords=GFAP"},{"String":"GTUBULIN","Alias":"gamma-tubulin","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=TUBG1&keywords=gamma,tubulin"},{"String":"IBA1","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=AIF1&keywords=IBA1"},{"String":"KERATIN","Alias":"pan-cytokeratin, pan-keratin","Link":"https://www.genecards.org/Search/Keyword?queryString=KERATIN"},{"String":"KI67","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MKI67&keywords=KI67"},{"String":"LAG3","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LAG3&keywords=LAG3"},{"String":"LAMINAC","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LMNA&keywords=LAMIN,AC"},{"String":"LAMINB","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LMNB1&keywords=LAMINB"},{"String":"PD-1","Alias":"PD1","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PDCD1&keywords=PD-1"},{"String":"PD-L1","Alias":"PDL1","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD274&keywords=PD-L1"},{"String":"CD19","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD19&keywords=CD19"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD11c"},{"String":"CD56","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=NCAM1&keywords=CD56"},{"String":"CD34","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD34&keywords=CD34"},{"String":"CD44","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD44&keywords=CD34"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD14"},{"String":"CD33","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD33&keywords=CD33"},{"String":"CD41","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGA2B&keywords=CD41"},{"String":"CD61","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGB3&keywords=CD61"},{"String":"CD62","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=SELP&keywords=CD62"},{"String":"CD146","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MCAM&keywords=CD146"},{"String":"CD1d","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD1D&keywords=CD1d"},{"String":"CD2","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD2&keywords=CD2"},{"String":"CD5","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD5&keywords=cd5"},{"String":"CD7","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD7&keywords=CD7"},{"String":"CD9","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD9&keywords=CD9"},{"String":"CD10","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MME&keywords=CD10"},{"String":"CD11A","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAL&keywords=CD11A"},{"String":"CD70","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD70&keywords=CD70"},{"String":"CD74","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD74&keywords=CD74"},{"String":"CD103","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAE&keywords=CD103"},{"String":"CD133","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PROM1&keywords=CD133"},{"String":"CD168","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=HMMR&keywords=CD168"}];
const cell_type_data = [{"String":"Natural Killer Cells","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/natural-killer-cells"},{"String":"B Cells","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/b-cells"},{"String":"Basophil","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/basophils"},{"String":"Helper T cell","Alias":"CD4+ T Cell","Link":"https://www.immunology.org/public-information/bitesized-immunology/células/cd4-t-cells"},{"String":"Cytotoxic T Cell","Alias":"CD8+ T Cell","Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/cd8-t-cells"},{"String":"Dendritic Cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/dendritic-cells"},{"String":"Eosinophils","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/eosinophils"},{"String":"Macrophage","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/macrophages"},{"String":"Mast Cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/mast-cells"},{"String":"Neutrophil","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/neutrophils"},{"String":"Regulatory T Cell","Alias":"Treg","Link":"https://www.immunology.org/public-information/bitesized-immunology/células/regulatory-t-cells-tregs"},{"String":"T follicular helper cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/t-follicular-helper-cells"},{"String":"bone marrow","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/%C3%B3rganos-y-tejidos/bone-marrow"},{"String":"lymph node","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/organs-and-tissues/lymph-node"},{"String":"complement system","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/sistemas-y-procesos/complement-system"},{"String":"phagocytosis","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/systems-and-processes/phagocytosis"}];
let marker_data = [{"String":"ARL13B","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ARL13B&keywords=ARL13B"},{"String":"ASMA","Alias":"A-SMA, a-SMA, alpha-SMA, α-SMA","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ACTA2&keywords=alpha,smooth,muscle,actin"},{"String":"BANF1","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=BANF1&keywords=BANF1"},{"String":"CD11B","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAM&keywords=CD11B"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD14"},{"String":"CD163","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD163&keywords=CD163"},{"String":"CD19","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD19&keywords=CD19"},{"String":"CD20","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MS4A1&keywords=CD20"},{"String":"CD21","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CR2&keywords=CD21"},{"String":"CD3D","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD3D&keywords=CD3D"},{"String":"CD4","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4&keywords=CD4"},{"String":"CD45","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PTPRC&keywords=CD45"},{"String":"CD45RB","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PTPRC&keywords=CD45RB"},{"String":"CD68","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD68&keywords=CD68"},{"String":"CD8A","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8A&keywords=CD8A"},{"String":"FOXP3","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=FOXP3&keywords=FOXP3"},{"String":"GFAP","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=GFAP&keywords=GFAP"},{"String":"GTUBULIN","Alias":"gamma-tubulin","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=TUBG1&keywords=gamma,tubulin"},{"String":"IBA1","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=AIF1&keywords=IBA1"},{"String":"KERATIN","Alias":"pan-cytokeratin, pan-keratin","Link":"https://www.genecards.org/Search/Keyword?queryString=KERATIN"},{"String":"KI67","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MKI67&keywords=KI67"},{"String":"LAG3","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LAG3&keywords=LAG3"},{"String":"LAMINAC","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LMNA&keywords=LAMIN,AC"},{"String":"LAMINB","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=LMNB1&keywords=LAMINB"},{"String":"PD-1","Alias":"PD1","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PDCD1&keywords=PD-1"},{"String":"PD-L1","Alias":"PDL1","Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD274&keywords=PD-L1"},{"String":"CD19","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD19&keywords=CD19"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD11c"},{"String":"CD56","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=NCAM1&keywords=CD56"},{"String":"CD34","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD34&keywords=CD34"},{"String":"CD44","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD44&keywords=CD34"},{"String":"CD14","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD14&keywords=CD14"},{"String":"CD33","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD33&keywords=CD33"},{"String":"CD41","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGA2B&keywords=CD41"},{"String":"CD61","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGB3&keywords=CD61"},{"String":"CD62","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=SELP&keywords=CD62"},{"String":"CD146","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MCAM&keywords=CD146"},{"String":"CD1d","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD1D&keywords=CD1d"},{"String":"CD2","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD2&keywords=CD2"},{"String":"CD5","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD5&keywords=cd5"},{"String":"CD7","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD7&keywords=CD7"},{"String":"CD9","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD9&keywords=CD9"},{"String":"CD10","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=MME&keywords=CD10"},{"String":"CD11A","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAL&keywords=CD11A"},{"String":"CD70","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD70&keywords=CD70"},{"String":"CD74","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=CD74&keywords=CD74"},{"String":"CD103","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGAE&keywords=CD103"},{"String":"CD133","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=PROM1&keywords=CD133"},{"String":"CD168","Alias":null,"Link":"https://www.genecards.org/cgi-bin/carddisp.pl?gene=HMMR&keywords=CD168"}];
let cell_type_data = [{"String":"Natural Killer Cells","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/natural-killer-cells"},{"String":"B Cells","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/b-cells"},{"String":"Basophil","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/basophils"},{"String":"Helper T cell","Alias":"CD4+ T Cell","Link":"https://www.immunology.org/public-information/bitesized-immunology/células/cd4-t-cells"},{"String":"Cytotoxic T Cell","Alias":"CD8+ T Cell","Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/cd8-t-cells"},{"String":"Dendritic Cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/dendritic-cells"},{"String":"Eosinophils","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/eosinophils"},{"String":"Macrophage","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/macrophages"},{"String":"Mast Cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/c%C3%A9lulas/mast-cells"},{"String":"Neutrophil","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/neutrophils"},{"String":"Regulatory T Cell","Alias":"Treg","Link":"https://www.immunology.org/public-information/bitesized-immunology/células/regulatory-t-cells-tregs"},{"String":"T follicular helper cell","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/cells/t-follicular-helper-cells"},{"String":"bone marrow","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/%C3%B3rganos-y-tejidos/bone-marrow"},{"String":"lymph node","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/organs-and-tissues/lymph-node"},{"String":"complement system","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/sistemas-y-procesos/complement-system"},{"String":"phagocytosis","Alias":null,"Link":"https://www.immunology.org/public-information/bitesized-immunology/systems-and-processes/phagocytosis"}];

const exhibitCSS = `
@import url("https://fonts.googleapis.com/css?family=Hind+Vadodara:500|Overpass:200,800");
Expand Down Expand Up @@ -3059,6 +3059,12 @@ const build_page_with_exhibit = function(exhibit, options) {

export const build_page = function(options) {

if (Array.isArray(options.markerData)) {
marker_data = options.markerData;
}
if (Array.isArray(options.cellTypeData)) {
cell_type_data = options.cellTypeData;
}
// define the marker and cell type links table
const marker_maps = get_links_alias(marker_data);
options.marker_links_map = marker_maps[0];
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
"build": "webpack --mode production"
},
"name": "minerva-browser",
"version": "2.14.2",
"version": "2.15.0",
"description": "A storytelling interface atop openseadragon",
"main": "index.js",
"repository": {
Expand Down

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