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glyphConfig.js
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// Set here the color scheme and the marker(glyph) shape for the gene panel you are working
// with. These gene-specific shapes come into action at the deep zoom levels, when Leaflet.js
// takes over.
//
// There is switch for that called zoomSwitch, see line 39 of index.js together with the moveend
// callback, see lines 459 and 511 of dapi.js.
//
// Outside this deep zoom zone all genes have the same shape, a solid circle, see
// line 11, stage_markers_patched.js
//
// Note that leaflet doesnt get on very well with lots and lots of datapoints, if you notice
// some slowness on the viewer maybe changing the zoomSwitch from its default value of 7 to 8
// will probably help.
//
// Only the following shapes are supported:
// star6
// star5
// diamond
// square
// triangleUp
// triangleDown
// triangleRight
// triangleLeft
// cross
// plus
// asterisk
// circle
// point
//
// These are designed in glyphPaths.js and introduced to the viewer from glyphs.js (no need to edit them
// unless you want to do an extra shape).
function glyphSettings()
{
var out = [
{gene: 'Snca', color: '#0000FF', glyphName: 'plus'},
{gene: 'Cplx2', color: '#0000FF', glyphName: 'point'},
{gene: 'Lhx6', color: '#0000FF', glyphName: 'square'},
{gene: 'Col25a1', color: '#0000FF', glyphName: 'triangleUp'},
{gene: 'Pnoc', color: '#0000FF', glyphName: 'triangleRight'},
{gene: 'Rab3c', color: '#0000FF', glyphName: 'triangleLeft'},
{gene: 'Gad1', color: '#0000FF', glyphName: 'star5'},
{gene: 'Slc6a1', color: '#0000FF', glyphName: 'star6'},
{gene: 'Th', color: '#00B3FF', glyphName: 'plus'},
{gene: 'Crhbp', color: '#00B3FF', glyphName: 'circle'},
{gene: 'Sst', color: '#00B3FF', glyphName: 'asterisk'},
{gene: 'Npy', color: '#00B3FF', glyphName: 'point'},
{gene: 'Synpr', color: '#00B3FF', glyphName: 'cross'},
{gene: 'Chodl', color: '#00B3FF', glyphName: 'square'},
{gene: 'Cort', color: '#00B3FF', glyphName: 'diamond'},
{gene: 'Reln', color: '#00B3FF', glyphName: 'triangleUp'},
{gene: 'Serpini1', color: '#00B3FF', glyphName: 'triangleLeft'},
{gene: 'Satb1', color: '#00B3FF', glyphName: 'triangleRight'},
{gene: 'Grin3a', color: '#00B3FF', glyphName: 'star5'},
{gene: 'Tac1', color: '#5C33FF', glyphName: 'circle'},
{gene: 'Pvalb', color: '#5C33FF', glyphName: 'asterisk'},
{gene: 'Kcnip2', color: '#5C33FF', glyphName: 'square'},
{gene: 'Thsd7a', color: '#5C33FF', glyphName: 'diamond'},
{gene: 'Cox6a2', color: '#5C33FF', glyphName: 'triangleDown'},
{gene: 'Chrm2', color: '#5C33FF', glyphName: 'star5'},
{gene: 'Id2', color: '#FF00E6', glyphName: 'plus'},
{gene: 'Hapln1', color: '#FF00E6', glyphName: 'circle'},
{gene: 'Gabrd', color: '#FF00E6', glyphName: 'asterisk'},
{gene: 'Cryab', color: '#FF00E6', glyphName: 'cross'},
{gene: 'Kit', color: '#FF00E6', glyphName: 'square'},
{gene: 'Ndnf', color: '#FF00E6', glyphName: 'diamond'},
{gene: 'Nos1', color: '#FF00E6', glyphName: 'triangleUp'},
{gene: 'Lamp5', color: '#FF00E6', glyphName: 'triangleRight'},
{gene: 'Cplx3', color: '#FF00E6', glyphName: 'star6'},
{gene: 'Cadps2', color: '#995C00', glyphName: 'circle'},
{gene: 'Cxcl14', color: '#995C00', glyphName: 'asterisk'},
{gene: 'Ntng1', color: '#995C00', glyphName: 'square'},
{gene: 'Cpne5', color: '#995C00', glyphName: 'diamond'},
{gene: 'Rgs12', color: '#995C00', glyphName: 'star6'},
{gene: 'Sncg', color: '#FF0000', glyphName: 'circle'},
{gene: 'Cnr1', color: '#FF0000', glyphName: 'asterisk'},
{gene: 'Cck', color: '#FF0000', glyphName: 'point'},
{gene: 'Trp53i11', color: '#FF0000', glyphName: 'cross'},
{gene: 'Sema3c', color: '#FF0000', glyphName: 'square'},
{gene: 'Syt6', color: '#FF0000', glyphName: 'triangleUp'},
{gene: 'Yjefn3', color: '#FF0000', glyphName: 'triangleDown'},
{gene: 'Rgs10', color: '#FF0000', glyphName: 'triangleRight'},
{gene: 'Nov', color: '#FF0000', glyphName: 'triangleLeft'},
{gene: 'Kctd12', color: '#FF0000', glyphName: 'star5'},
{gene: 'Slc17a8', color: '#FF0000', glyphName: 'star6'},
{gene: 'Tac2', color: '#FFC700', glyphName: 'plus'},
{gene: 'Npy2r', color: '#FFC700', glyphName: 'circle'},
{gene: 'Calb2', color: '#FFC700', glyphName: 'asterisk'},
{gene: 'Htr3a', color: '#FFC700', glyphName: 'point'},
{gene: 'Slc5a7', color: '#FFC700', glyphName: 'cross'},
{gene: 'Penk', color: '#FFC700', glyphName: 'square'},
{gene: 'Pthlh', color: '#FFC700', glyphName: 'triangleUp'},
{gene: 'Vip', color: '#FFC700', glyphName: 'triangleDown'},
{gene: 'Crh', color: '#FFC700', glyphName: 'triangleRight'},
{gene: 'Qrfpr', color: '#FFC700', glyphName: 'star5'},
{gene: 'Zcchc12', color: '#96B38F', glyphName: 'plus'},
{gene: 'Calb1', color: '#96B38F', glyphName: 'asterisk'},
{gene: 'Vsnl1', color: '#96B38F', glyphName: 'point'},
{gene: 'Tmsb10', color: '#96B38F', glyphName: 'diamond'},
{gene: 'Rbp4', color: '#96B38F', glyphName: 'triangleDown'},
{gene: 'Fxyd6', color: '#96B38F', glyphName: 'triangleUp'},
{gene: '6330403K07Rik', color: '#96B38F', glyphName: 'triangleLeft'},
{gene: 'Scg2', color: '#96B38F', glyphName: 'triangleRight'},
{gene: 'Gap43', color: '#96B38F', glyphName: 'star5'},
{gene: 'Nrsn1', color: '#96B38F', glyphName: 'star6'},
{gene: 'Gda', color: '#407F59', glyphName: 'plus'},
{gene: 'Bcl11b', color: '#407F59', glyphName: 'circle'},
{gene: 'Rgs4', color: '#407F59', glyphName: 'asterisk'},
{gene: 'Slc24a2', color: '#407F59', glyphName: 'point'},
{gene: 'Lphn2', color: '#407F59', glyphName: 'cross'},
{gene: 'Adgrl2', color: '#407F59', glyphName: 'cross'},
{gene: 'Map2', color: '#407F59', glyphName: 'square'},
{gene: 'Prkca', color: '#407F59', glyphName: 'diamond'},
{gene: 'Cdh13', color: '#407F59', glyphName: 'triangleUp'},
{gene: 'Atp1b1', color: '#407F59', glyphName: 'triangleDown'},
{gene: 'Pde1a', color: '#407F59', glyphName: 'triangleLeft'},
{gene: 'Calm2', color: '#407F59', glyphName: 'triangleRight'},
{gene: 'Sema3e', color: '#407F59', glyphName: 'star6'},
{gene: 'Nrn1', color: '#00FF00', glyphName: 'asterisk'},
{gene: 'Pcp4', color: '#00FF00', glyphName: 'point'},
{gene: 'Rprm', color: '#00FF00', glyphName: 'plus'},
{gene: 'Enpp2', color: '#00FF00', glyphName: 'cross'},
{gene: 'Rorb', color: '#00FF00', glyphName: 'circle'},
{gene: 'Rasgrf2', color: '#00FF00', glyphName: 'square'},
{gene: 'Wfs1', color: '#00FF00', glyphName: 'diamond'},
{gene: 'Fos', color: '#00FF00', glyphName: 'triangleRight'},
{gene: 'Plcxd2', color: '#00FF00', glyphName: 'triangleDown'},
{gene: 'Crym', color: '#00FF00', glyphName: 'triangleLeft'},
{gene: '3110035E14Rik', color: '#00FF00', glyphName: 'triangleUp'},
{gene: 'Foxp2', color: '#00FF00', glyphName: 'star5'},
{gene: 'Pvrl3', color: '#00FF00', glyphName: 'star6'},
{gene: 'Neurod6', color: '#44B300', glyphName: 'plus'},
{gene: 'Nr4a2', color: '#44B300', glyphName: 'circle'},
{gene: 'Cux2', color: '#44B300', glyphName: 'asterisk'},
{gene: 'Kcnk2', color: '#44B300', glyphName: 'point'},
{gene: 'Arpp21', color: '#44B300', glyphName: 'square'},
{gene: 'Enc1', color: '#44B300', glyphName: 'triangleDown'},
{gene: 'Fam19a1', color: '#44B300', glyphName: 'triangleRight'},
{gene: 'Vim', color: '#FFFFFF', glyphName: 'asterisk'},
{gene: 'Slc1a2', color: '#FFFFFF', glyphName: 'point'},
{gene: 'Pax6', color: '#FFFFFF', glyphName: 'square'},
{gene: 'Plp1', color: '#FFFFFF', glyphName: 'cross'},
{gene: 'Mal', color: '#FFFFFF', glyphName: 'plus'},
{gene: 'Aldoc', color: '#FFFFFF', glyphName: 'circle'},
{gene: 'Actb', color: '#FFFFFF', glyphName: 'triangleDown'},
{gene: 'Sulf2', color: '#FFFFFF', glyphName: 'star5'},
// Do not remove this. If a gene is missing from the settings above, use these as default
{gene: 'Generic', color: '#0000FF', glyphName: 'circle'},
];
return out
}