@sjcrh/proteinpaint-client 2.79.5 → 2.79.7-0

package/dist/singlecell-QAUS3LFJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/singlecell.js"],
-  "sourcesContent": ["import * as client from './client'\nimport * as d3 from 'd3'\nimport { interpolatePlasma } from 'd3-scale-chromatic'\nimport { axisTop, axisBottom } from 'd3-axis'\nimport { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { gene_searchbox, findgenemodel_bysymbol } from './gene'\nimport { legend_newrow } from './block.legend'\nimport { schemeCategory20 } from '#common/legacy-d3-polyfill'\n\n/*\n********************** EXPORTED\ninit()\n********************** INTERNAL\nsequence of calls by init()\n\tload_json()\n\tvalidate_obj()\n\tinit_view() // init three.js scene, camera and renderer\n\t\tadd_scriptTag() // add three.js scripts\n\tinit_controlpanel()\n\tpcd_pipeline() // query data from csv file and create pcd file to be rendered\n\t\tload_cell_pcd() // query data for category with color as auto/custom or gene expression\n\t\trender_cloud() // remove old points and create point cloud using PCDLoader() \n\t\trender_controlpanel() // render control panel for category or gene expression\n\tmake_legend() // make legend if predefined in json file as image file\n\nmake_zoom_panel() // change camera.fov when zoom in / out \nmake_menu() // menu when clicked on category or gene button at top of config\nmake_settings() //settings panel to change background, pointsize, reset, screenshot and zoom\nheatmap_menu() // menu to enter multiple genes and select category\n\tmake_heatmap() // make heatmap for multiple genes and category\nmake_plot() // for single gene\n\tmake_violin_plot() // make violin plot for single gene expression vs category\n\tmake_box_plot() // make box plot for single gene expression vs category\n*/\n\nexport async function init(arg, holder) {\n\ttry {\n\t\tconst obj = await load_json(arg)\n\t\tvalidate_obj(obj)\n\n\t\tobj.genome = arg.genome\n\t\tobj.holder = holder.style('position', 'relative')\n\t\tawait init_view(obj)\n\t\tinit_controlpanel(obj)\n\t\tawait pcd_pipeline(obj)\n\t\tmake_legend(arg, obj)\n\t} catch (e) {\n\t\tclient.sayerror(holder, e.message || e)\n\t}\n}\n\nasync function load_json(arg) {\n\tif (!arg.jsonfile) throw '.jsonfile missing'\n\tconst tmp = await client.dofetch('textfile', { file: arg.jsonfile })\n\tif (tmp.error) throw tmp.error\n\treturn JSON.parse(tmp.text)\n}\n\nfunction validate_obj(obj) {\n\tif (!obj.cells) throw '.cells{} missing'\n\tif (!obj.cells.file) throw '.cells.file missing'\n\tif (!obj.cells.axis2columnidx) throw '.cells.axis2columnidx missing'\n\tif (obj.cells.categories) {\n\t\tif (!Array.isArray(obj.cells.categories)) throw '.cells.categories should be an array'\n\t\tif (obj.cells.categories.length == 0) throw '.cells.categories[] is empty array'\n\t\tfor (const c of obj.cells.categories) {\n\t\t\tif (!Number.isInteger(c.columnidx)) throw 'columnidx missing from category ' + c\n\t\t\tif (c.autocolor) {\n\t\t\t\tc.autocolor = scaleOrdinal(schemeCategory20)\n\t\t\t}\n\t\t}\n\t\tif (!Number.isInteger(obj.use_category_index)) {\n\t\t\tobj.use_category_index = 0\n\t\t}\n\t\tif (!obj.cells.categories[obj.use_category_index]) throw 'use_category_index out of bound'\n\t\tif (!obj.cells.categories[obj.use_category_index].hidden_types)\n\t\t\tobj.cells.categories[obj.use_category_index].hidden_types = []\n\t}\n\tif (obj.gene_expression) {\n\t\tif (!obj.gene_expression.file) throw '.gene_expression.file missing'\n\t\tif (!Number.isInteger(obj.cells.barcodecolumnidx))\n\t\t\tthrow '.gene_expression in use but .cells.barcodecolumnidx is missing'\n\t}\n\tif (!obj.width) obj.width = window.innerWidth * 0.9\n\tif (!obj.height) obj.height = window.innerHeight * 0.9\n}\n\nasync function pcd_pipeline(obj) {\n\tif (Number.isInteger(obj.use_category_index)) {\n\t\tif (!obj.cells.categories[obj.use_category_index].hidden_types)\n\t\t\tobj.cells.categories[obj.use_category_index].hidden_types = []\n\t}\n\tconst data = await load_cell_pcd(obj)\n\n\t// get sphere radius from max of x, y and z coordinates and assign it to camera and controls\n\tobj.data_sphere_r = data.data_sphere_r\n\tif (!obj.camera.position.z) {\n\t\tobj.camera.position.z = obj.data_sphere_r * 3\n\t\tobj.controls.maxDistance = obj.data_sphere_r * 4\n\t\tobj.controls.minDistance = obj.data_sphere_r / 10\n\t}\n\tconst enc = new TextEncoder()\n\tconst pcd_buffer = enc.encode(data.pcddata).buffer\n\trender_cloud(obj, pcd_buffer)\n\trender_controlpanel(obj, data)\n\n\tanimate()\n\n\tfunction animate() {\n\t\trequestAnimationFrame(animate)\n\t\tobj.controls.update()\n\t\tobj.renderer.render(obj.scene, obj.camera)\n\t}\n}\n\nasync function load_cell_pcd(obj) {\n\t/*\nto load a new pcd file\ncall this when using a new category,\nor selected a gene for overlaying\n*/\n\tconst wait = obj.holder\n\t\t.append('div')\n\t\t.style('position', 'absolute')\n\t\t.style('top', 0)\n\t\t.style('left', 0)\n\t\t.style('padding', '10px')\n\t\t.style('font-size', '1.5rem')\n\t\t.text('Loading data...')\n\n\tconst arg = {\n\t\tgenome: obj.genome.name,\n\t\ttextfile: obj.cells.file,\n\t\tdelimiter: obj.cells.delimiter || '\\t',\n\t\tgetpcd: {\n\t\t\tcoord: obj.cells.axis2columnidx\n\t\t}\n\t}\n\n\tif (Number.isInteger(obj.use_category_index)) {\n\t\t/*\n\t\tthis is the array index of obj.categories[]\n\t\tto use this category for coloring cells\n\t\t*/\n\t\tif (!obj.cells.categories) throw 'using category index but cells.categories[] missing'\n\t\tconst cat = obj.cells.categories[obj.use_category_index]\n\t\tif (!cat) throw 'category array index out of bound'\n\t\targ.getpcd.category_index = cat.columnidx\n\n\t\tif (cat.autocolor) {\n\t\t\t// if categories are autocolored and not defined in config\n\t\t\targ.getpcd.category_autocolor = true\n\t\t\tif (cat.values_count) arg.getpcd.values_count = cat.values_count\n\t\t} else if (cat.values) {\n\t\t\t//if colors are defined in config\n\t\t\targ.getpcd.category_customcolor = true\n\t\t\targ.getpcd.cat_values = cat.values\n\t\t} else {\n\t\t\tif (!cat.autocolor && !cat.values) throw 'categories.values[] are not defined'\n\t\t\tthrow 'unknow coloring scheme for category ' + cat.name\n\t\t}\n\t\tif (cat.hidden_types) {\n\t\t\targ.hidden_types = cat.hidden_types\n\t\t}\n\t\tif (obj.background_color) {\n\t\t\targ.background_color = obj.background_color\n\t\t}\n\t\t//set flags for ordering legend\n\t\tif (!cat.customorder) {\n\t\t\t// if categories are autoordered and not defined in config\n\t\t\targ.getpcd.category_autoorder = true\n\t\t} else if (cat.customorder && cat.values) {\n\t\t\t//if order are defined in config\n\t\t\targ.getpcd.category_customorder = true\n\t\t\targ.getpcd.cat_values = cat.values\n\t\t} else {\n\t\t\tif (cat.customorder && !cat.values) throw 'categories.values[] are not defined'\n\t\t\tthrow 'unknow ordering scheme for category ' + cat.name\n\t\t}\n\t\t// update menu_button here\n\t\tobj.menu_button.html(cat.name + '&nbsp;&nbsp;&#9660;')\n\t} else if (Number.isInteger(obj.use_gene_index)) {\n\t\tconst gene = obj.gene_expression.genes[obj.use_gene_index]\n\t\tobj.menu_button.html('Gene : ' + gene.gene + '&nbsp;&nbsp;&#9660;')\n\t\targ.getpcd.gene_expression = {\n\t\t\tfile: obj.gene_expression.file,\n\t\t\tbarcodecolumnidx: obj.cells.barcodecolumnidx,\n\t\t\tchr: gene.chr,\n\t\t\tstart: gene.start,\n\t\t\tstop: gene.stop,\n\t\t\tautoscale: true,\n\t\t\tgenename: gene.gene,\n\t\t\tcolor_min: obj.gene_expression.color_min,\n\t\t\tcolor_max: obj.gene_expression.color_max\n\t\t}\n\t\tif (obj.gene_expression.color_no_exp) arg.getpcd.gene_expression.color_no_exp = obj.gene_expression.color_no_exp\n\t} else {\n\t\tthrow 'unknown method to color the cells'\n\t}\n\n\treturn client.dofetch('singlecell', arg).then(data => {\n\t\tif (data.error) throw data.error\n\n\t\twait.remove()\n\t\treturn data\n\t})\n}\n\nasync function init_view(obj) {\n\t// TODO only load below if to do 3d\n\tawait add_scriptTag('/static/js/three.js')\n\tawait add_scriptTag('/static/js/loaders/PCDLoader.js')\n\tawait add_scriptTag('/static/js/controls/TrackballControls.js')\n\tawait add_scriptTag('/static/js/WebGL.js')\n\n\tif (WEBGL.isWebGLAvailable() === false) {\n\t\tobj.holder.node().appendChild(WEBGL.getWebGLErrorMessage())\n\t\treturn\n\t}\n\n\tobj.scene = new THREE.Scene()\n\tif (obj.background_color) {\n\t\tobj.scene.background = new THREE.Color(obj.background_color)\n\t} else {\n\t\tobj.scene.background = new THREE.Color(0xffffff)\n\t}\n\n\tconst default_zoom = obj.default_zoom ? 100 - obj.default_zoom : 45\n\t// camera parameters explaination: https://observablehq.com/@grantcuster/understanding-scale-and-the-three-js-perspective-camera\n\tobj.camera = new THREE.PerspectiveCamera(default_zoom, obj.width / obj.height, 0.1, 1000)\n\n\tobj.camera.position.x = obj.canvas_2d ? 0 : 20\n\tobj.camera.position.y = obj.canvas_2d ? 0 : -10\n\n\tif (obj.canvas_2d) {\n\t\tobj.camera.up.set(0, 1, 0)\n\t} else {\n\t\tobj.camera.up.set(0, 0, 1)\n\t}\n\n\tobj.controls = new THREE.TrackballControls(obj.camera)\n\n\tobj.controls.rotateSpeed = obj.canvas_2d ? 0 : 2.0\n\tobj.controls.zoomSpeed = obj.canvas_2d ? 3.0 : 0.7\n\tobj.controls.panSpeed = obj.canvas_2d ? 3.0 : 0.7\n\n\tobj.controls.noZoom = true\n\tobj.controls.noPan = false\n\n\tobj.controls.staticMoving = true\n\tobj.controls.dynamicDampingFactor = 0.3\n\n\tobj.scene.add(obj.camera)\n\n\tobj.renderer = new THREE.WebGLRenderer({ antialias: true, preserveDrawingBuffer: true })\n\tobj.renderer.setPixelRatio(window.devicePixelRatio)\n\tobj.renderer.setSize(obj.width, obj.height)\n\tobj.renderer.domElement.style.backgroundColor = '#ffffff'\n\tobj.renderer.domElement.style.border = 'solid #dddddd 2px'\n\n\tobj.holder\n\t\t.style('display', 'inline-block')\n\t\t.style('position', 'relative')\n\t\t.node()\n\t\t.appendChild(obj.renderer.domElement)\n\n\tobj.renderer.render(obj.scene, obj.camera)\n}\n\nfunction render_cloud(obj, pcd_buffer) {\n\t// remove old points before adding new\n\tobj.scene.children.forEach(function(v, i) {\n\t\tif (v.material) {\n\t\t\tv.material.dispose()\n\t\t\tv.geometry.dispose()\n\t\t\tobj.scene.remove(v)\n\t\t}\n\t})\n\n\t// add new points using loader\n\tconst loader = new THREE.PCDLoader()\n\tconst points = loader.parse(pcd_buffer, '')\n\n\tif (obj.point_size) {\n\t\tpoints.material.size = obj.point_size\n\t} else {\n\t\tpoints.material.size = obj.canvas_2d ? 0.3 : 0.05\n\t}\n\n\tobj.scene.add(points)\n\tobj.center = points.geometry.boundingSphere.center\n\tobj.controls.target.set(obj.center.x, obj.center.y, obj.center.z)\n\tobj.controls.update()\n}\n\nfunction init_controlpanel(obj) {\n\tobj.menu = new client.Menu()\n\tobj.menu.d.style('padding', '3px')\n\n\tobj.settings = new client.Menu()\n\tobj.settings.d.style('padding', '3px')\n\n\tconst panel = obj.holder\n\t\t.append('div')\n\t\t.style('padding', '10px')\n\t\t.style('position', 'absolute')\n\t\t.style('border-radius', '5px')\n\t\t.style('top', '20px')\n\t\t.style('right', '20px')\n\t\t.style('background-color', '#dddddd')\n\n\tobj.menu_button = panel\n\t\t.append('button')\n\t\t.style('display', 'inline-block')\n\t\t.style('padding', '4px')\n\t\t.on('click', () => make_menu(obj))\n\n\tconst minimize_btn = (obj.minimize_btn = panel\n\t\t.append('div')\n\t\t.style('margin-left', '10px')\n\t\t.style('display', 'inline-block')\n\t\t.style('padding-left', '0px')\n\t\t.style('padding-right', '2px')\n\t\t.style('float', 'right')\n\t\t.style('font-size', '.6em')\n\t\t.classed('active', obj.menu_minimized ? true : false)\n\t\t.text(obj.menu_minimized ? ' SHOW' : ' HIDE')\n\t\t.on('click', () => {\n\t\t\tobj.minimize_btn.classed('active', obj.minimize_btn.classed('active') ? false : true)\n\t\t\tif (obj.minimize_btn.classed('active')) {\n\t\t\t\tobj.minimize_btn.text(' SHOW')\n\t\t\t\tobj.menu_output.style('display', 'none')\n\t\t\t} else {\n\t\t\t\tobj.minimize_btn.text(' HIDE')\n\t\t\t\tobj.menu_output.style('display', 'block')\n\t\t\t}\n\t\t})\n\t\t.on('mouseover', () => {\n\t\t\tminimize_btn.style('text-decoration', 'underline')\n\t\t})\n\t\t.on('mouseout', () => {\n\t\t\tminimize_btn.style('text-decoration', 'none')\n\t\t}))\n\n\tobj.use_background_color = 0\n\n\tconst config_btn = (obj.settings_btn = panel\n\t\t.append('div')\n\t\t.style('margin-left', '10px')\n\t\t.style('display', 'inline-block')\n\t\t.style('padding-left', '3px')\n\t\t.style('padding-right', '3px')\n\t\t.style('float', 'right')\n\t\t.style('font-size', '.6em')\n\t\t.text('CONFIG')\n\t\t.on('click', () => make_settings(obj))\n\t\t.on('mouseover', () => {\n\t\t\tconfig_btn.style('text-decoration', 'underline')\n\t\t})\n\t\t.on('mouseout', () => {\n\t\t\tconfig_btn.style('text-decoration', 'none')\n\t\t}))\n\n\tobj.menu_output = panel\n\t\t.append('div')\n\t\t.style('margin-top', '10px')\n\t\t.style('display', obj.menu_minimized ? 'none' : 'block')\n\n\tobj.show_zoom = true //flag to show zoom div under legend div\n}\n\nfunction render_controlpanel(obj, data) {\n\tobj.menu_output.selectAll('*').remove()\n\n\tif (data.category2color) {\n\t\t/*\n\t\tshowing the color legend for the current category\n\t\tTODO\n\t\t\tpredefined colors\n\t\t\tat each type, show checkbox for filtering cells\n\t\t*/\n\t\tconst top_row = obj.menu_output.append('div').style('margin', '2px')\n\n\t\tconst select_all_checkbox = top_row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.style('margin-right', '10px')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.on('change', () => {\n\t\t\t\tif (select_all_checkbox.node().checked) {\n\t\t\t\t\tobj.cells.categories[obj.use_category_index].hidden_types = []\n\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t} else {\n\t\t\t\t\tfor (const type in data.category2color) {\n\t\t\t\t\t\tobj.cells.categories[obj.use_category_index].hidden_types.push(type)\n\t\t\t\t\t}\n\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t}\n\t\t\t})\n\n\t\tif (obj.cells.categories[obj.use_category_index].hidden_types.length == 0) {\n\t\t\tselect_all_checkbox.property('checked', 1)\n\t\t}\n\n\t\ttop_row\n\t\t\t.append('span')\n\t\t\t.text('Select All')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.attr('font-family', client.font)\n\n\t\tfor (const type in data.category2color) {\n\t\t\t// div for each label\n\t\t\tconst row = obj.menu_output.append('div').style('margin', '2px')\n\n\t\t\tconst checkbox = row\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.property('checked', 1)\n\t\t\t\t.style('margin-right', '10px')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tif (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {\n\t\t\t\t\t\tconst index = obj.cells.categories[obj.use_category_index].hidden_types.indexOf(type)\n\t\t\t\t\t\tif (index !== -1) obj.cells.categories[obj.use_category_index].hidden_types.splice(index, 1)\n\t\t\t\t\t\tcheckbox.property('checked', 1)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tobj.cells.categories[obj.use_category_index].hidden_types.push(type)\n\t\t\t\t\t}\n\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t})\n\n\t\t\tif (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {\n\t\t\t\tcheckbox.property('checked', 0)\n\t\t\t}\n\n\t\t\t// square color for the label\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('height', '15px')\n\t\t\t\t.style('width', '15px')\n\t\t\t\t.style('background-color', data.category2color[type])\n\t\t\t\t.style('margin-right', '10px')\n\n\t\t\t//label text\n\t\t\trow\n\t\t\t\t.append('span')\n\t\t\t\t.text(type)\n\t\t\t\t.attr('font-family', client.font)\n\n\t\t\trow\n\t\t\t\t.append('span')\n\t\t\t\t.html('&nbsp;n=' + data.categorycount[type])\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('float', 'right')\n\t\t\t\t.style('color', '#777')\n\t\t}\n\t} else if (data.maxexpvalue) {\n\t\t// for gene expression data show gradient scale with unit\n\n\t\tconst scale_height = 30\n\t\tconst scale_width = 150\n\n\t\tconst scale_div = obj.menu_output\n\t\t\t.append('div')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('width', '120px')\n\t\t\t.style('height', '100px')\n\n\t\tscale_div\n\t\t\t.append('div')\n\t\t\t.text('Gene Expression ' + obj.gene_expression.datatype)\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('width', '150px')\n\t\t\t.style('margin-bottom', '20px')\n\n\t\tconst svg = scale_div.append('svg').append('g')\n\n\t\tconst colorRange = [obj.gene_expression.color_max, obj.gene_expression.color_min]\n\n\t\tconst colorScale = scaleLinear()\n\t\t\t.range(colorRange)\n\t\t\t.domain([data.minexpvalue, data.maxexpvalue])\n\n\t\tconst defs = svg.append('defs')\n\n\t\tconst linearGradient = defs.append('linearGradient').attr('id', 'linear-gradient')\n\t\t// .attr('gradientTransform', 'rotate(90)')\n\n\t\tlinearGradient\n\t\t\t.append('stop')\n\t\t\t.attr('offset', '0%')\n\t\t\t.attr('stop-color', colorScale(data.maxexpvalue))\n\n\t\tlinearGradient\n\t\t\t.append('stop')\n\t\t\t.attr('offset', '100%')\n\t\t\t.attr('stop-color', colorScale(data.minexpvalue))\n\n\t\tsvg\n\t\t\t.append('rect')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('width', scale_width)\n\t\t\t.attr('height', scale_height)\n\t\t\t.attr('transform', 'translate(12, 0)')\n\t\t\t.style('fill', 'url(#linear-gradient)')\n\n\t\tconst y = scaleLinear()\n\t\t\t.range([0, scale_width])\n\t\t\t.domain([data.minexpvalue, data.maxexpvalue])\n\n\t\tconst legendAxis = axisBottom()\n\t\t\t.scale(y)\n\t\t\t.ticks(5)\n\n\t\tsvg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'legend axis')\n\t\t\t.attr('transform', 'translate(12,' + scale_height + ')')\n\t\t\t.call(legendAxis)\n\n\t\tconst stats_div = obj.menu_output\n\t\t\t.append('div')\n\t\t\t.style('padding-bottom', '20px')\n\t\t\t.style('text-align', 'center')\n\n\t\tstats_div\n\t\t\t.append('p')\n\t\t\t.style('font-size', '13px')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.html('<b>Cells with Expression Data</b> ')\n\n\t\tstats_div\n\t\t\t.append('p')\n\t\t\t.style('font-size', '13px')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.html(data.numbercellwithgeneexp + ' / ' + data.numbercelltotal)\n\n\t\tconst no_exp_div = stats_div\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.style('margin-top', '10px')\n\n\t\tno_exp_div\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('height', '15px')\n\t\t\t.style('width', '15px')\n\t\t\t.style('background-color', obj.gene_expression.color_no_exp ? obj.gene_expression.color_no_exp : '#2C2C2C')\n\t\t\t.style('margin-right', '10px')\n\n\t\tno_exp_div\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('font-size', '13px')\n\t\t\t.html(' Cells without Expression')\n\n\t\t// Show option for Boxplot for Gene Expression by catagories\n\t\tconst boxplot_div = obj.menu_output.append('div')\n\n\t\tboxplot_div\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.style('padding', '5px')\n\t\t\t.html('Violinplot / Boxplot of </br> Expression by')\n\n\t\tconst boxplot_cat_select = boxplot_div.append('select').style('display', 'block')\n\n\t\tboxplot_cat_select\n\t\t\t.append('option')\n\t\t\t.attr('value', 'none')\n\t\t\t.text('-- Select--')\n\n\t\tif (obj.cells.categories) {\n\t\t\tobj.cells.categories.forEach((category, i) => {\n\t\t\t\tboxplot_cat_select\n\t\t\t\t\t.append('option')\n\t\t\t\t\t.attr('value', category.columnidx)\n\t\t\t\t\t.text(category.name)\n\t\t\t})\n\t\t}\n\t\tboxplot_cat_select.on('change', () => {\n\t\t\tconst gene = obj.gene_expression.genes[obj.use_gene_index]\n\t\t\tconst cat = obj.cells.categories[parseInt(boxplot_cat_select.node().selectedIndex) - 1]\n\t\t\tconst arg = {\n\t\t\t\tgenome: obj.genome.name,\n\t\t\t\tgetgeneboxplot: {\n\t\t\t\t\texpfile: obj.gene_expression.file,\n\t\t\t\t\tchr: gene.chr,\n\t\t\t\t\tstart: gene.start,\n\t\t\t\t\tstop: gene.stop,\n\t\t\t\t\tgenename: gene.gene,\n\t\t\t\t\tcellfile: obj.cells.file,\n\t\t\t\t\tbarcodecolumnidx: obj.cells.barcodecolumnidx,\n\t\t\t\t\tcategorycolumnidx: parseInt(boxplot_cat_select.node().value),\n\t\t\t\t\tdelimiter: obj.cells.delimiter || '\\t',\n\t\t\t\t\tcategory_customorder: cat.customorder && cat.values ? true : false,\n\t\t\t\t\tcategory_autoorder: !cat.customorder ? true : false,\n\t\t\t\t\tcat_values: cat.values,\n\t\t\t\t\tvalues_count: cat.values_count\n\t\t\t\t}\n\t\t\t}\n\t\t\tclient.dofetch('singlecell', arg).then(data => {\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tobj.box_plot = new client.Menu()\n\t\t\t\tmake_plot(data, obj, boxplot_cat_select.node().value)\n\t\t\t})\n\t\t})\n\t}\n\n\tmake_zoom_panel(obj)\n}\n\nfunction make_zoom_panel(obj) {\n\tif (obj.show_zoom) {\n\t\t// zoom in / zoom out\n\t\tconst zoom_div = obj.menu_output\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.text('Zoom')\n\t\t\t.style('margin', '10px 5px 5px 5px')\n\t\t\t.style('padding-top', '10px')\n\t\t\t.style('border-top', '1px solid #929292')\n\n\t\tconst zoom_hide_btn = zoom_div\n\t\t\t.append('div')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding-left', '0px')\n\t\t\t.style('padding-right', '2px')\n\t\t\t.style('float', 'right')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.text('MOVE TO CONFIG')\n\t\t\t.on('click', () => {\n\t\t\t\tzoom_div.node().remove()\n\t\t\t\tobj.show_zoom = false\n\t\t\t})\n\t\t\t.on('mouseover', () => {\n\t\t\t\tzoom_hide_btn.style('text-decoration', 'underline')\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tzoom_hide_btn.style('text-decoration', 'none')\n\t\t\t})\n\n\t\tobj.zoom_slider = zoom_div\n\t\t\t.append('input')\n\t\t\t.style('display', 'block')\n\t\t\t.style('padding', '5px')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 1)\n\t\t\t.attr('max', 100)\n\t\t\t.attr('value', obj.camera.fov)\n\t\t\t.style('direction', 'rtl')\n\t\t\t.on('change', () => {\n\t\t\t\tobj.camera.fov = parseInt(obj.zoom_slider.node().value)\n\t\t\t\tobj.camera.updateProjectionMatrix()\n\t\t\t})\n\t\t\t.on('mousedown', event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t})\n\t}\n}\n\nfunction make_menu(obj) {\n\tobj.menu.clear().showunder(obj.menu_button.node())\n\n\tif (obj.cells.categories) {\n\t\tobj.cells.categories.forEach((category, i) => {\n\t\t\tif (i != obj.use_category_index) {\n\t\t\t\t// add option\n\t\t\t\tobj.menu.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text(category.name)\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\tobj.menu.hide()\n\n\t\t\t\t\t\tobj.use_category_index = i\n\t\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t\t})\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.style('display', category.values_count ? 'inline-block' : 'none')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t.style('float', 'right')\n\t\t\t\t\t.style('color', '#777')\n\t\t\t\t\t.style('padding', '3px 5px')\n\t\t\t\t\t.html(category.values_count ? '&nbsp;n=' + category.values_count : '')\n\t\t\t}\n\t\t})\n\t}\n\n\tif (obj.gene_expression) {\n\t\t// add option\n\t\tobj.menu.d\n\t\t\t.append('div')\n\t\t\t.text('Gene expression')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.on('click', () => {\n\t\t\t\tobj.menu.clear()\n\n\t\t\t\tconst gene_search_div = obj.menu.d.append('div').style('padding', '10px')\n\n\t\t\t\tgene_searchbox({\n\t\t\t\t\tdiv: gene_search_div.append('div'),\n\t\t\t\t\tresultdiv: gene_search_div.append('div'),\n\t\t\t\t\tgenome: obj.genome.name,\n\t\t\t\t\tcallback: async genename => {\n\t\t\t\t\t\tconst gmlst = await findgenemodel_bysymbol(obj.genome.name, genename)\n\t\t\t\t\t\tif (gmlst && gmlst[0]) {\n\t\t\t\t\t\t\tconst gm = gmlst[0]\n\t\t\t\t\t\t\tif (!obj.gene_expression.genes) obj.gene_expression.genes = []\n\t\t\t\t\t\t\tconst geneidx = obj.gene_expression.genes.findIndex(i => i.gene == genename)\n\t\t\t\t\t\t\tif (geneidx == -1) {\n\t\t\t\t\t\t\t\tobj.gene_expression.genes.push({\n\t\t\t\t\t\t\t\t\tgene: genename,\n\t\t\t\t\t\t\t\t\tchr: gm.chr,\n\t\t\t\t\t\t\t\t\tstart: gm.start,\n\t\t\t\t\t\t\t\t\tstop: gm.stop\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\tobj.use_gene_index = obj.gene_expression.genes.length - 1\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tobj.use_gene_index = geneidx\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tobj.use_category_index = null\n\t\t\t\t\t\tobj.menu.hide()\n\n\t\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\n\t\t// menu option for multi-gene heatmap\n\t\tobj.menu.d\n\t\t\t.append('div')\n\t\t\t.text('Multi-Gene Heatmap')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.on('click', () => {\n\t\t\t\theatmap_menu(obj)\n\t\t\t})\n\n\t\tif (obj.gene_expression.genes) {\n\t\t\tif (obj.gene_expression.genes.length > 1) {\n\t\t\t\tobj.menu.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t\t.text('Previously Selected')\n\t\t\t}\n\n\t\t\tobj.gene_expression.genes.forEach((gene, i) => {\n\t\t\t\tif (i != obj.use_gene_index) {\n\t\t\t\t\t// add option\n\t\t\t\t\tobj.menu.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.text('Gene : ' + gene.gene)\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\t\tobj.menu.hide()\n\n\t\t\t\t\t\t\tobj.use_category_index = null\n\t\t\t\t\t\t\tobj.use_gene_index = i\n\n\t\t\t\t\t\t\tpcd_pipeline(obj)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n}\n\nfunction make_settings(obj) {\n\tobj.settings.clear().showunder(obj.settings_btn.node())\n\n\t// Background Color change option\n\tconst back_color_div = obj.settings.d\n\t\t.append('div')\n\t\t.style('display', 'block')\n\t\t.text('Background Color')\n\t\t.style('margin', '5px')\n\n\tconst black_div = back_color_div\n\t\t.append('div')\n\t\t.style('margin', '5px')\n\t\t.style('display', 'block')\n\n\tconst name = Math.random(),\n\t\tidblack = Math.random(),\n\t\tidwhite = Math.random()\n\n\tconst inputblack = black_div\n\t\t.append('input')\n\t\t.attr('type', 'radio')\n\t\t.style('display', 'inline-block')\n\t\t.attr('name', name)\n\t\t.attr('id', idblack)\n\t\t.on('change', toggle_background)\n\n\tblack_div\n\t\t.append('label')\n\t\t.style('display', 'inline-block')\n\t\t.style('font-size', '.8em')\n\t\t.text('Black')\n\t\t.style('padding-left', '10px')\n\t\t.attr('for', idblack)\n\n\tconst white_div = back_color_div\n\t\t.append('div')\n\t\t.style('margin', '5px')\n\t\t.style('display', 'block')\n\n\tconst inputwhite = white_div\n\t\t.append('input')\n\t\t.attr('type', 'radio')\n\t\t.style('display', 'inline-block')\n\t\t.attr('name', name)\n\t\t.attr('id', idwhite)\n\t\t.on('change', toggle_background)\n\n\twhite_div\n\t\t.append('label')\n\t\t.style('display', 'inline-block')\n\t\t.style('font-size', '.8em')\n\t\t.text('White')\n\t\t.style('padding-left', '10px')\n\t\t.attr('for', idwhite)\n\n\tif (obj.use_background_color == 0) {\n\t\tinputwhite.property('checked', 1)\n\t} else {\n\t\tinputblack.property('checked', 1)\n\t}\n\n\tfunction toggle_background() {\n\t\tconst isblack = obj.background_color == 'black'\n\t\tobj.scene.background = new THREE.Color(isblack ? 0xffffff : 0x000000)\n\t\tobj.use_background_color = isblack ? 0 : 1\n\t\tobj.background_color = isblack ? 'white' : 'black'\n\t}\n\t// point size change\n\tconst point_size_div = obj.settings.d\n\t\t.append('div')\n\t\t.style('display', 'block')\n\t\t.text('Point Size')\n\t\t.style('margin', '20px 5px')\n\n\tconst point_size_slider = point_size_div\n\t\t.append('input')\n\t\t.style('display', 'block')\n\t\t.style('padding', '5px')\n\t\t.attr('type', 'range')\n\t\t.attr('min', 1)\n\t\t.attr('max', 70)\n\t\t.attr('value', obj.scene.children[1].material.size * 100)\n\t\t.on('change', () => {\n\t\t\tobj.scene.children[1].material.size = point_size_slider.node().value / 100\n\t\t})\n\n\tif (obj.show_zoom == false) {\n\t\t// zoom in / zoom out\n\t\tconst zoom_div = obj.settings.d\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.text('Zoom')\n\t\t\t.style('margin', '20px 5px')\n\n\t\tconst zoom_hide_btn = zoom_div\n\t\t\t.append('div')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding-left', '0px')\n\t\t\t.style('padding-right', '2px')\n\t\t\t.style('float', 'right')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.html('MOVE TO </br>LEGEND PANEL')\n\t\t\t.on('click', () => {\n\t\t\t\tzoom_div.node().remove()\n\t\t\t\tobj.show_zoom = true\n\t\t\t\tmake_zoom_panel(obj)\n\t\t\t})\n\t\t\t.on('mouseover', () => {\n\t\t\t\tzoom_hide_btn.style('text-decoration', 'underline')\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tzoom_hide_btn.style('text-decoration', 'none')\n\t\t\t})\n\n\t\tobj.zoom_slider = zoom_div\n\t\t\t.append('input')\n\t\t\t.style('display', 'block')\n\t\t\t.style('padding', '5px')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 5)\n\t\t\t.attr('max', 70)\n\t\t\t.attr('value', obj.camera.fov)\n\t\t\t.style('direction', 'rtl')\n\t\t\t.on('change', () => {\n\t\t\t\tobj.camera.fov = parseInt(obj.zoom_slider.node().value)\n\t\t\t\tobj.camera.updateProjectionMatrix()\n\t\t\t})\n\t}\n\n\t// info for panning\n\tobj.settings.d\n\t\t.append('div')\n\t\t.style('margin', '5px')\n\t\t.text('Panning')\n\n\tobj.settings.d\n\t\t.append('div')\n\t\t.style('font-size', '.8em')\n\t\t.style('text-align', 'center')\n\t\t.style('margin-bottom', '10px')\n\t\t.html('<p style=\"margin:3px;\">Right mouse click </br>+ Mouse move</p>')\n\n\tif (!obj.canvas_2d) {\n\t\t// info for roatation\n\t\tobj.settings.d\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px')\n\t\t\t.text('Rotate')\n\n\t\tobj.settings.d\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('margin-bottom', '10px')\n\t\t\t.html('<p style=\"margin:3px;\">Left mouse click </br>+ Mouse move</p>')\n\t}\n\n\t// reset button\n\tobj.settings.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Reset view')\n\t\t.style('width', '80px')\n\t\t.style('margin', 'auto')\n\t\t.style('margin-top', '15px')\n\t\t.style('margin-bottom', '15px')\n\t\t.on('click', () => {\n\t\t\t// reset background checkbox\n\t\t\tinputwhite.property('checked', 1)\n\t\t\tobj.scene.background = new THREE.Color(obj.background_color ? obj.background_color : 0xffffff)\n\n\t\t\t// reset point size\n\t\t\tpoint_size_slider.node().value = obj.point_size ? obj.point_size * 100 : obj.canvas_2d ? 30 : 5\n\t\t\tobj.scene.children[1].material.size = obj.point_size ? obj.point_size : obj.canvas_2d ? 0.3 : 0.05\n\n\t\t\t//reset zoom and camera\n\t\t\tobj.camera.position.z = obj.data_sphere_r * 3\n\t\t\tobj.camera.position.x = obj.canvas_2d ? 0 : 20\n\t\t\tobj.camera.position.y = obj.canvas_2d ? 0 : -10\n\n\t\t\tconst cam_fov_default = 45\n\t\t\tobj.camera.fov = parseInt(cam_fov_default)\n\t\t\tobj.camera.updateProjectionMatrix()\n\t\t\tobj.zoom_slider.node().value = cam_fov_default\n\n\t\t\tif (obj.canvas_2d) {\n\t\t\t\tobj.camera.up.set(0, 1, 0)\n\t\t\t} else {\n\t\t\t\tobj.camera.up.set(0, 0, 1)\n\t\t\t}\n\n\t\t\t//reset panning\n\t\t\tobj.controls.target.set(obj.center.x, obj.center.y, obj.center.z)\n\t\t})\n\n\t// screenshot button\n\tconst screenshot_btn = obj.settings.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('padding', '5px')\n\t\t.style('width', '80px')\n\t\t.style('margin', 'auto')\n\t\t.style('margin-top', '15px')\n\t\t.style('margin-bottom', '15px')\n\t\t.html('<b>&#10697;</b> Capture')\n\t\t.on('mousedown', () => {\n\t\t\tconst imgData = obj.renderer.domElement.toDataURL()\n\n\t\t\tlet imgNode = document.createElement('img')\n\t\t\timgNode.src = imgData\n\t\t\t// document.body.appendChild(imgNode)\n\t\t\tscreenshot_btn\n\t\t\t\t.append('span')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.html(\n\t\t\t\t\t'<a download=\"scRNA_' +\n\t\t\t\t\t\tnew Date().toLocaleString() +\n\t\t\t\t\t\t'.png\" href=\"' +\n\t\t\t\t\t\timgNode.src +\n\t\t\t\t\t\t'\" title=\"ImageName\">Camera</a>'\n\t\t\t\t)\n\t\t\t// download_btn.node().click()\n\t\t})\n\t\t.on('mouseup', () => {\n\t\t\tscreenshot_btn\n\t\t\t\t.select('a')\n\t\t\t\t.node()\n\t\t\t\t.click()\n\t\t\tscreenshot_btn.selectAll('span').remove()\n\t\t})\n}\n\nfunction heatmap_menu(obj) {\n\tobj.menu.clear()\n\tobj.gene_expression.heatmap_genes = []\n\tobj.use_heatmap_category_index = null\n\n\tconst heatmap_menu_div = obj.menu.d\n\t\t.append('div')\n\t\t.style('display', 'block')\n\t\t.style('padding', '10px')\n\n\tconst genes_div = heatmap_menu_div.append('div').style('display', 'block')\n\n\tconst gene_search_div = genes_div\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('vertical-align', 'top')\n\t\t.style('padding', '10px')\n\n\tgene_search_div\n\t\t.append('div')\n\t\t.style('display', 'block')\n\t\t.style('padding-bottom', '5px')\n\t\t.text('Add Genes')\n\n\tgene_search_div\n\t\t.append('textarea')\n\t\t.attr('rows', '4')\n\t\t.attr('cols', '20')\n\t\t.attr('placeholder', 'Type gene names seperated by space')\n\n\t// Show option for Boxplot for Gene Expression by catagories\n\tconst catagory_div = heatmap_menu_div.append('div')\n\n\tcatagory_div\n\t\t.append('div')\n\t\t.style('display', 'block')\n\t\t.style('padding-bottom', '5px')\n\t\t.style('padding-left', '10px')\n\t\t.text('Heatmap by')\n\n\tconst cat_select = catagory_div\n\t\t.append('select')\n\t\t.style('display', 'block')\n\t\t.style('margin-left', '10px')\n\n\tcat_select\n\t\t.append('option')\n\t\t.attr('value', 'none')\n\t\t.text('-- Select--')\n\n\tif (obj.cells.categories) {\n\t\tobj.cells.categories.forEach((category, i) => {\n\t\t\tcat_select\n\t\t\t\t.append('option')\n\t\t\t\t.attr('value', category.columnidx)\n\t\t\t\t.text(category.name)\n\t\t})\n\t}\n\n\tcat_select.on('change', () => {\n\t\tobj.use_heatmap_category_index = parseInt(cat_select.node().value)\n\t})\n\n\t// button to generate heatmap\n\theatmap_menu_div\n\t\t.append('button')\n\t\t.text('Heatmap')\n\t\t.style('display', 'block')\n\t\t.style('float', 'right')\n\t\t.style('margin', '5px')\n\t\t.on('click', async () => {\n\t\t\tconst input_genelist = gene_search_div.select('textarea').node().value\n\t\t\tconst genelist = input_genelist.split(' ')\n\t\t\tfor (const gene of genelist) {\n\t\t\t\tconst gmlst = await findgenemodel_bysymbol(obj.genome.name, gene)\n\t\t\t\tif (gmlst && gmlst[0]) {\n\t\t\t\t\tconst gm = gmlst[0]\n\t\t\t\t\tif (!obj.gene_expression.heatmap_genes) obj.gene_expression.heatmap_genes = []\n\t\t\t\t\tconst geneidx = obj.gene_expression.heatmap_genes.findIndex(i => i.gene == gene)\n\t\t\t\t\tif (geneidx == -1) {\n\t\t\t\t\t\tobj.gene_expression.heatmap_genes.push({\n\t\t\t\t\t\t\tgene: gene,\n\t\t\t\t\t\t\tchr: gm.chr,\n\t\t\t\t\t\t\tstart: gm.start,\n\t\t\t\t\t\t\tstop: gm.stop\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst arg = {\n\t\t\t\tgenome: obj.genome.name,\n\t\t\t\tgetheatmap: {\n\t\t\t\t\texpfile: obj.gene_expression.file,\n\t\t\t\t\tgene_list: obj.gene_expression.heatmap_genes,\n\t\t\t\t\tcellfile: obj.cells.file,\n\t\t\t\t\tbarcodecolumnidx: obj.cells.barcodecolumnidx,\n\t\t\t\t\tcategorycolumnidx: parseInt(cat_select.node().value),\n\t\t\t\t\tdelimiter: obj.cells.delimiter || '\\t'\n\t\t\t\t}\n\t\t\t}\n\t\t\tclient.dofetch('singlecell', arg).then(data => {\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tobj.menu.hide()\n\t\t\t\tmake_heatmap(data, obj, cat_select.node().value)\n\t\t\t})\n\t\t})\n}\n\nfunction make_plot(data, obj, colidx) {\n\tconst gene = obj.gene_expression.genes[obj.use_gene_index]\n\tconst pane = client.newpane({ x: 600, y: 400 })\n\tconst cat = obj.cells.categories.find(x => x.columnidx == colidx)\n\tpane.header.text('Violinplot/Boxplot for ' + gene.gene + ' Expression by ' + cat.name)\n\n\tconst control_panel = pane.pane.append('div').style('margin', '10px 10px 10px 15px')\n\n\tconst svg = pane.pane.append('svg').style('margin', '10px')\n\n\t//toggle between violin and Boxplot\n\tconst plot_select = control_panel.append('select').style('display', 'inline-block')\n\n\tplot_select\n\t\t.append('option')\n\t\t.attr('value', 'violin')\n\t\t.text('Violin Plot')\n\n\tplot_select\n\t\t.append('option')\n\t\t.attr('value', 'box')\n\t\t.text('Box Plot')\n\n\tplot_select.on('change', () => {\n\t\tapply()\n\t})\n\n\t//toggle between cells with/without expression to be included in plot\n\tconst cell_select_div = control_panel\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('padding-left', '15px')\n\t\t.text('Cells without expression')\n\n\tconst cell_select = cell_select_div\n\t\t.append('select')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-left', '5px')\n\n\tcell_select\n\t\t.append('option')\n\t\t.attr('value', 'include')\n\t\t.text('Include')\n\n\tcell_select\n\t\t.append('option')\n\t\t.attr('value', 'exclude')\n\t\t.text('Exclude')\n\n\tcell_select.on('change', () => {\n\t\tapply()\n\t})\n\n\tmake_violin_plot(data, svg)\n\n\tfunction apply() {\n\t\tconst gene = obj.gene_expression.genes[obj.use_gene_index]\n\t\tconst arg = {\n\t\t\tgenome: obj.genome.name,\n\t\t\tgetgeneboxplot: {\n\t\t\t\texpfile: obj.gene_expression.file,\n\t\t\t\tchr: gene.chr,\n\t\t\t\tstart: gene.start,\n\t\t\t\tstop: gene.stop,\n\t\t\t\tgenename: gene.gene,\n\t\t\t\tcellfile: obj.cells.file,\n\t\t\t\tbarcodecolumnidx: obj.cells.barcodecolumnidx,\n\t\t\t\tcategorycolumnidx: parseInt(colidx),\n\t\t\t\tdelimiter: obj.cells.delimiter || '\\t',\n\t\t\t\tcategory_customorder: cat.customorder && cat.values ? true : false,\n\t\t\t\tcategory_autoorder: !cat.customorder ? true : false,\n\t\t\t\tcat_values: cat.values,\n\t\t\t\tvalues_count: cat.values_count\n\t\t\t}\n\t\t}\n\n\t\tif (cell_select.node().value == 'exclude') {\n\t\t\targ.getgeneboxplot.exclude_cells = true\n\t\t}\n\t\tclient.dofetch('singlecell', arg).then(data => {\n\t\t\tif (data.error) throw data.error\n\t\t\tif (plot_select.node().value == 'box') make_box_plot(data, svg)\n\t\t\telse if (plot_select.node().value == 'violin') make_violin_plot(data, svg)\n\t\t})\n\t}\n}\n\nfunction make_violin_plot(data, svg) {\n\tsvg.selectAll('*').remove()\n\n\tlet box_height = 50,\n\t\tbox_width = 200,\n\t\tbarspace = 2,\n\t\taxis_height = 30\n\n\tconst label_width = get_max_labelwidth(data.boxplots, svg)\n\n\tconst x_scale = scaleLinear()\n\t\t.range([0, box_width])\n\t\t.domain([data.minexpvalue, data.maxexpvalue])\n\n\tconst y_scale = scaleLinear()\n\t\t.range([box_height, 0])\n\t\t.domain([0, 1])\n\n\tconst svg_height = data.boxplots.length * (box_height + barspace) + axis_height\n\tconst svg_width = box_width + label_width + 20\n\n\tsvg\n\t\t.transition()\n\t\t.attr('width', svg_width)\n\t\t.attr('height', svg_height)\n\n\tif (data.boxplots) {\n\t\tdata.boxplots.forEach((boxplot, i) => {\n\t\t\tconst g = svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', 'translate(' + label_width + ',' + (i * (box_height + barspace) + axis_height) + ')')\n\n\t\t\tconst xlabel = g\n\t\t\t\t.append('text')\n\t\t\t\t.text(boxplot.category + ' (' + boxplot.numberofcells + ')')\n\t\t\t\t.attr('transform', 'translate(-4,' + box_height / 2 + ')')\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('font-size', 15)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\n\t\t\tif (boxplot.density) {\n\t\t\t\tconst density_max = Math.max(...boxplot.density)\n\n\t\t\t\tconst line = d3\n\t\t\t\t\t.line()\n\t\t\t\t\t.x(function(d, j) {\n\t\t\t\t\t\treturn x_scale((j * data.maxexpvalue) / boxplot.density.length)\n\t\t\t\t\t}) // set the x values for the line generator\n\t\t\t\t\t.y(function(d) {\n\t\t\t\t\t\treturn y_scale(d / density_max) / 2\n\t\t\t\t\t}) // set the y values for the line generator\n\t\t\t\t\t.curve(d3.curveMonotoneX) // apply smoothing to the line\n\n\t\t\t\tconst area = d3\n\t\t\t\t\t.area()\n\t\t\t\t\t.x(function(d, j) {\n\t\t\t\t\t\treturn x_scale((j * data.maxexpvalue) / boxplot.density.length)\n\t\t\t\t\t})\n\t\t\t\t\t.y0(function(d) {\n\t\t\t\t\t\tconst temp = y_scale(d / density_max) / 2\n\t\t\t\t\t\treturn box_height - temp\n\t\t\t\t\t})\n\t\t\t\t\t.y1(function(d) {\n\t\t\t\t\t\treturn y_scale(d / density_max) / 2\n\t\t\t\t\t})\n\t\t\t\t\t.curve(d3.curveMonotoneX)\n\n\t\t\t\tg.append('path')\n\t\t\t\t\t.datum(boxplot.density)\n\t\t\t\t\t.attr('class', 'area')\n\t\t\t\t\t.attr('d', area)\n\t\t\t\t\t// .style('fill','lightsteelblue')\n\t\t\t\t\t.style('fill', boxplot.color)\n\t\t\t\t\t.style('stroke', 'black')\n\t\t\t\t\t.style('stroke-width', 0.5)\n\t\t\t}\n\t\t})\n\n\t\tconst legendAxis = axisTop()\n\t\t\t.scale(x_scale)\n\t\t\t.ticks(5)\n\n\t\tsvg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'legend axis')\n\t\t\t.attr('transform', 'translate(' + label_width + ',' + (axis_height - 10) + ')')\n\t\t\t.call(legendAxis)\n\t}\n}\n\nfunction make_box_plot(data, svg) {\n\tsvg.selectAll('*').remove()\n\n\tlet box_height = 36,\n\t\tbox_width = 200,\n\t\tbarspace = 16,\n\t\taxis_height = 30\n\n\tconst label_width = get_max_labelwidth(data.boxplots, svg)\n\n\tconst x_scale = scaleLinear()\n\t\t.range([0, box_width])\n\t\t.domain([data.minexpvalue, data.maxexpvalue])\n\n\tconst y_scale = scaleLinear()\n\t\t.range([box_height, 0])\n\t\t.domain([0, 1])\n\n\tconst svg_height = data.boxplots.length * (box_height + barspace) + axis_height\n\tconst svg_width = box_width + label_width + 20\n\n\tsvg\n\t\t.transition()\n\t\t.attr('width', svg_width)\n\t\t.attr('height', svg_height)\n\n\tif (data.boxplots) {\n\t\tdata.boxplots.forEach((boxplot, i) => {\n\t\t\tconst g = svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', 'translate(' + label_width + ',' + (i * (box_height + barspace) + axis_height) + ')')\n\n\t\t\tconst xlabel = g\n\t\t\t\t.append('text')\n\t\t\t\t.text(boxplot.category + ' (' + boxplot.numberofcells + ')')\n\t\t\t\t.attr('transform', 'translate(-4,' + box_height / 2 + ')')\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('font-size', 15)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\n\t\t\tif (boxplot.p75) {\n\t\t\t\tg.append('line')\n\t\t\t\t\t.attr('x1', x_scale(boxplot.w1))\n\t\t\t\t\t.attr('y1', box_height / 2)\n\t\t\t\t\t.attr('x2', x_scale(boxplot.w2))\n\t\t\t\t\t.attr('y2', box_height / 2)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('stroke', 'black')\n\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', x_scale(boxplot.p25))\n\t\t\t\t\t.attr('y', 0)\n\t\t\t\t\t.attr('width', x_scale(boxplot.p75 - boxplot.p25))\n\t\t\t\t\t.attr('height', box_height)\n\t\t\t\t\t// .attr('fill','#901739')\n\t\t\t\t\t.attr('fill', boxplot.color)\n\n\t\t\t\tg.append('line')\n\t\t\t\t\t.attr('x1', x_scale(boxplot.w1))\n\t\t\t\t\t.attr('y1', 0)\n\t\t\t\t\t.attr('x2', x_scale(boxplot.w1))\n\t\t\t\t\t.attr('y2', box_height)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('stroke', 'black')\n\n\t\t\t\tg.append('line')\n\t\t\t\t\t.attr('x1', x_scale(boxplot.p50))\n\t\t\t\t\t.attr('y1', 0)\n\t\t\t\t\t.attr('x2', x_scale(boxplot.p50))\n\t\t\t\t\t.attr('y2', box_height)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('stroke', 'white')\n\n\t\t\t\tg.append('line')\n\t\t\t\t\t.attr('x1', x_scale(boxplot.w2))\n\t\t\t\t\t.attr('y1', 0)\n\t\t\t\t\t.attr('x2', x_scale(boxplot.w2))\n\t\t\t\t\t.attr('y2', box_height)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('stroke', 'black')\n\n\t\t\t\tif (boxplot.out) {\n\t\t\t\t\tfor (const outlier of boxplot.out) {\n\t\t\t\t\t\tg.append('circle')\n\t\t\t\t\t\t\t.attr('cx', x_scale(outlier.value))\n\t\t\t\t\t\t\t.attr('cy', box_height / 2)\n\t\t\t\t\t\t\t.attr('r', 2)\n\t\t\t\t\t\t\t.attr('fill', '#901739')\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tconst legendAxis = axisTop()\n\t\t\t.scale(x_scale)\n\t\t\t.ticks(5)\n\n\t\tsvg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'legend axis')\n\t\t\t.attr('transform', 'translate(' + label_width + ',' + (axis_height - 10) + ')')\n\t\t\t.call(legendAxis)\n\t}\n}\n\nfunction make_heatmap(data, obj, colidx) {\n\tconst pane = client.newpane({ x: 600, y: 400 })\n\tconst cat = obj.cells.categories.find(x => x.columnidx == colidx)\n\tpane.header.text('Heatmap for Gene Expression by ' + cat.name)\n\tconst svg = pane.pane.append('svg').style('margin', '10px')\n\n\t// labels of x and y axis\n\tlet gene_list = []\n\tfor (const gene of data.gene_heatmap) gene_list.push(gene.genename)\n\n\t//find max value for heatmap\n\tlet means = []\n\tdata.gene_heatmap.forEach((gene, i) => {\n\t\tdata.gene_heatmap[i].heatmap.forEach(category => {\n\t\t\tmeans.push(category.mean)\n\t\t})\n\t})\n\tconst max_mean = Math.max(...means)\n\n\tlet categories = []\n\tfor (const category of data.gene_heatmap[0].heatmap)\n\t\tcategories.push(category.category + ' (' + category.numberofcells + ')')\n\n\tlet box_height = 20,\n\t\tbox_width = 80,\n\t\tbarspace = 2,\n\t\tgene_lable_height = 30,\n\t\tlegend_width = 60\n\n\tconst label_width = get_max_labelwidth(data.gene_heatmap[0].heatmap, svg)\n\n\tconst svg_height = (box_height + barspace) * categories.length + gene_lable_height\n\tconst svg_width = (box_width + barspace) * gene_list.length + label_width + legend_width + 20\n\n\tsvg\n\t\t.transition()\n\t\t.attr('width', svg_width)\n\t\t.attr('height', svg_height)\n\n\t// Build X scales and axis:\n\tconst x_scale = d3\n\t\t.scaleBand()\n\t\t.range([0, (box_width + barspace) * gene_list.length])\n\t\t.domain(gene_list)\n\t\t.padding(0.05)\n\n\tsvg\n\t\t.append('g')\n\t\t.style('font-size', 15)\n\t\t.attr('transform', 'translate(' + label_width + ',0)')\n\t\t.call(d3.axisBottom(x_scale).tickSize(0))\n\t\t.select('.domain')\n\t\t.remove()\n\n\t// Build Y scales and axis:\n\tconst y_scale = d3\n\t\t.scaleBand()\n\t\t.range([(box_height + barspace) * categories.length, 0])\n\t\t.domain(categories)\n\t\t.padding(0.05)\n\n\tsvg\n\t\t.append('g')\n\t\t.style('font-size', 15)\n\t\t.attr('transform', 'translate(' + label_width + ',' + gene_lable_height + ')')\n\t\t.call(d3.axisLeft(y_scale).tickSize(0))\n\t\t.select('.domain')\n\t\t.remove()\n\n\t// Build color scale\n\tvar myColor = d3\n\t\t.scaleSequential()\n\t\t.interpolator(interpolatePlasma)\n\t\t.domain([0, max_mean])\n\n\tconst div = pane.pane\n\t\t.append('div')\n\t\t.style('position', 'absolute')\n\t\t.attr('class', 'tooltip')\n\t\t.style('background-color', 'white')\n\t\t.style('border', 'solid')\n\t\t.style('border-width', '2px')\n\t\t.style('border-radius', '5px')\n\t\t.style('padding', '5px')\n\t\t.style('opacity', 0)\n\n\tdata.gene_heatmap.forEach((gene, i) => {\n\t\tdata.gene_heatmap[i].heatmap.forEach((category, j) => {\n\t\t\tconst g = svg.append('g').attr('transform', 'translate(' + label_width + ',' + gene_lable_height + ')')\n\n\t\t\tg.append('rect')\n\t\t\t\t.attr('x', x_scale(gene.genename))\n\t\t\t\t.attr('y', y_scale(category.category + ' (' + category.numberofcells + ')'))\n\t\t\t\t.attr('width', x_scale.bandwidth())\n\t\t\t\t.attr('height', y_scale.bandwidth())\n\t\t\t\t.style('fill', myColor(category.mean))\n\t\t\t\t.style('stroke-width', 4)\n\t\t\t\t.style('stroke', 'none')\n\t\t\t\t.style('opacity', 0.8)\n\t\t\t\t//tooltip\n\t\t\t\t.on('mouseover', function(event) {\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.transition()\n\t\t\t\t\t\t.duration(200)\n\t\t\t\t\t\t.style('opacity', 0.9)\n\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.html('Mean Expression: ' + category.mean)\n\t\t\t\t\t\t.style('left', d3.pointer(event, this)[0] + 70 + 'px')\n\t\t\t\t\t\t.style('top', d3.pointer(event, this)[1] + 20 + 'px')\n\t\t\t\t})\n\t\t\t\t.on('mouseout', function() {\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.transition()\n\t\t\t\t\t\t.duration(500)\n\t\t\t\t\t\t.style('opacity', 0)\n\t\t\t\t})\n\t\t})\n\t})\n\tconst legend_data = myColor.ticks(10).reverse()\n\tlegend_data.unshift(max_mean.toFixed(2))\n\n\t// Add a legend for the color values\n\tconst legend = 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-  "names": ["data", "gene"]
-}

package/dist/snp-A2YNGQSD.js

@@ -1,70 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-A3GQXDSC.js";
-import "./chunk-ALPXXDQD.js";
-import "./chunk-ROQ5WSLC.js";
-import "./chunk-452UVSLH.js";
-import {
-  Menu
-} from "./chunk-7YY2KB6H.js";
-import "./chunk-2BM5YZ6X.js";
-import "./chunk-WFANY24Z.js";
-import "./chunk-BT2NCQ7T.js";
-import "./chunk-XNPZE2WZ.js";
-import "./chunk-WMK7VUYQ.js";
-import "./chunk-ZRUQHHLI.js";
-import "./chunk-JASS6SUY.js";
-import "./chunk-NUYFQ7WK.js";
-import "./chunk-P7BTNMOS.js";
-import "./chunk-5IJCZCP7.js";
-import "./chunk-CKF26VJ7.js";
-import "./chunk-Y6SKTI7D.js";
-import "./chunk-F3OQE4AZ.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat)
-      throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-export {
-  SearchHandler
-};
-//# sourceMappingURL=snp-A2YNGQSD.js.map

package/dist/snp-A2YNGQSD.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/snp.ts"],
-  "sourcesContent": ["import { Menu } from '#dom/menu'\nimport { addGeneSearchbox } from '../../dom/genesearch.ts'\n\nexport class SearchHandler {\n\tcallback: any\n\n\tinit(opts) {\n\t\tthis.callback = opts.callback\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: opts.holder,\n\t\t\tsearchOnly: 'snp',\n\t\t\tallowVariant: true,\n\t\t\tcallback: () => this.selectSnp(geneSearch)\n\t\t})\n\t}\n\n\tasync selectSnp(geneSearch) {\n\t\tconst { chr, ref, alt, fromWhat } = geneSearch\n\t\tif (!chr || !ref || !alt || !fromWhat) throw 'missing chr, ref, alt, or fromWhat of snp'\n\t\tlet start: number, stop: number\n\t\tif (!geneSearch.start && !geneSearch.stop) {\n\t\t\tif (geneSearch.pos) {\n\t\t\t\t// coordinate is .pos if input to geneSearch was\n\t\t\t\t// in variant/hgvs format\n\t\t\t\t// TODO: harmonize geneSearch output (also see TODO below)\n\t\t\t\tstart = geneSearch.pos - 1\n\t\t\t\tstop = geneSearch.pos\n\t\t\t} else {\n\t\t\t\tthrow 'missing coordinate of snp'\n\t\t\t}\n\t\t} else {\n\t\t\tstart = geneSearch.start\n\t\t\tstop = geneSearch.stop\n\t\t}\n\t\tconst term = {\n\t\t\tid: fromWhat,\n\t\t\tchr,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\tname: fromWhat,\n\t\t\tref,\n\t\t\talt: typeof alt == 'string' ? [alt] : alt, // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays\n\t\t\ttype: 'snp'\n\t\t}\n\t\tthis.callback(term)\n\t}\n}\n"],
-  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;AAGO,IAAM,gBAAN,MAAoB;AAAA,EAG1B,KAAK,MAAM;AACV,SAAK,WAAW,KAAK;AACrB,UAAM,aAAa,iBAAiB;AAAA,MACnC,KAAK,IAAI,KAAK,EAAE,SAAS,MAAM,CAAC;AAAA,MAChC,QAAQ,KAAK;AAAA,MACb,KAAK,KAAK;AAAA,MACV,YAAY;AAAA,MACZ,cAAc;AAAA,MACd,UAAU,MAAM,KAAK,UAAU,UAAU;AAAA,IAC1C,CAAC;AAAA,EACF;AAAA,EAEA,MAAM,UAAU,YAAY;AAC3B,UAAM,EAAE,KAAK,KAAK,KAAK,SAAS,IAAI;AACpC,QAAI,CAAC,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC;AAAU,YAAM;AAC7C,QAAI,OAAe;AACnB,QAAI,CAAC,WAAW,SAAS,CAAC,WAAW,MAAM;AAC1C,UAAI,WAAW,KAAK;AAInB,gBAAQ,WAAW,MAAM;AACzB,eAAO,WAAW;AAAA,MACnB,OAAO;AACN,cAAM;AAAA,MACP;AAAA,IACD,OAAO;AACN,cAAQ,WAAW;AACnB,aAAO,WAAW;AAAA,IACnB;AACA,UAAM,OAAO;AAAA,MACZ,IAAI;AAAA,MACJ;AAAA,MACA;AAAA,MACA;AAAA,MACA,MAAM;AAAA,MACN;AAAA,MACA,KAAK,OAAO,OAAO,WAAW,CAAC,GAAG,IAAI;AAAA;AAAA,MACtC,MAAM;AAAA,IACP;AACA,SAAK,SAAS,IAAI;AAAA,EACnB;AACD;",
-  "names": []
-}

package/dist/snp-UQSHCWCJ.js

@@ -1,79 +0,0 @@
-import {
-  getHandler
-} from "./chunk-UIQRT242.js";
-import "./chunk-2JPSZLBQ.js";
-import {
-  set_hiddenvalues
-} from "./chunk-EY7JFZ4D.js";
-import "./chunk-CLHA5AEH.js";
-import "./chunk-252GVCUB.js";
-import "./chunk-7KFEDC2T.js";
-import "./chunk-A3GQXDSC.js";
-import "./chunk-6XR2LO7D.js";
-import "./chunk-PWTXVCZ4.js";
-import "./chunk-FCPSU6WB.js";
-import "./chunk-O32YEJMI.js";
-import "./chunk-FOSTUUJG.js";
-import "./chunk-PGCZMKZL.js";
-import "./chunk-EG3MKQQH.js";
-import "./chunk-L7QWRU5Z.js";
-import "./chunk-JVUJSWZ2.js";
-import "./chunk-JV3G5Q3X.js";
-import "./chunk-ALPXXDQD.js";
-import "./chunk-CTQFEFIV.js";
-import "./chunk-RKJGIOIF.js";
-import "./chunk-P64DWRTC.js";
-import "./chunk-ROQ5WSLC.js";
-import "./chunk-452UVSLH.js";
-import "./chunk-7YY2KB6H.js";
-import "./chunk-2BM5YZ6X.js";
-import "./chunk-WFANY24Z.js";
-import {
-  copyMerge
-} from "./chunk-BT2NCQ7T.js";
-import "./chunk-XNPZE2WZ.js";
-import "./chunk-WMK7VUYQ.js";
-import "./chunk-ZRUQHHLI.js";
-import "./chunk-JASS6SUY.js";
-import "./chunk-NUYFQ7WK.js";
-import "./chunk-P7BTNMOS.js";
-import "./chunk-5IJCZCP7.js";
-import "./chunk-CKF26VJ7.js";
-import "./chunk-Y6SKTI7D.js";
-import "./chunk-F3OQE4AZ.js";
-
-// termsetting/handlers/snp.ts
-async function getHandler2(self) {
-  return getHandler(self);
-}
-async function fillTW(tw, vocabApi, defaultQ = null) {
-  if (typeof tw.term !== "object")
-    throw "tw.term is not an object";
-  if (!tw.term.id || !tw.term.name)
-    throw "missing snp id/name";
-  if (!tw.term.chr || !Number.isInteger(tw.term.start) || !Number.isInteger(tw.term.stop))
-    throw "incomplete position information";
-  if (!tw.term.ref || !tw.term.alt)
-    "missing allele information";
-  if (!Object.keys(tw.q).includes("type"))
-    tw.q.type = "values";
-  if (!tw.term.groupsetting)
-    tw.term.groupsetting = { disabled: false };
-  if (tw.q.type == "predefined-groupset") {
-    if (!Number.isInteger(tw.q.predefined_groupset_idx))
-      throw "predefined_groupset_idx is not an integer";
-  }
-  if (tw.q.type == "custom-groupset") {
-    if (!tw.q.customset)
-      throw "invalid customset";
-  }
-  if (defaultQ) {
-    copyMerge(tw.q, defaultQ);
-  }
-  set_hiddenvalues(tw.q, tw.term);
-}
-export {
-  fillTW,
-  getHandler2 as getHandler
-};
-//# sourceMappingURL=snp-UQSHCWCJ.js.map

package/dist/snp-UQSHCWCJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/snp.ts"],
-  "sourcesContent": ["import type { SnpTW, SnpQ, VocabApi } from '#types'\nimport { getHandler as getCategoricalHandler } from './categorical.ts'\nimport { copyMerge } from '#rx'\nimport { set_hiddenvalues } from '../termsetting.ts'\n\nexport async function getHandler(self) {\n\treturn getCategoricalHandler(self)\n}\n\nexport async function fillTW(tw: SnpTW, vocabApi: VocabApi, defaultQ: SnpQ | null = null) {\n\tif (typeof tw.term !== 'object') throw 'tw.term is not an object'\n\tif (!tw.term.id || !tw.term.name) throw 'missing snp id/name'\n\tif (!tw.term.chr || !Number.isInteger(tw.term.start) || !Number.isInteger(tw.term.stop))\n\t\tthrow 'incomplete position information'\n\tif (!tw.term.ref || !tw.term.alt) 'missing allele information'\n\n\tif (!Object.keys(tw.q).includes('type')) tw.q.type = 'values'\n\tif (!tw.term.groupsetting) tw.term.groupsetting = { disabled: false }\n\tif (tw.q.type == 'predefined-groupset') {\n\t\tif (!Number.isInteger(tw.q.predefined_groupset_idx)) throw 'predefined_groupset_idx is not an integer'\n\t}\n\tif (tw.q.type == 'custom-groupset') {\n\t\tif (!tw.q.customset) throw 'invalid customset'\n\t}\n\n\tif (defaultQ) {\n\t\t// merge defaultQ into tw.q\n\t\tcopyMerge(tw.q, defaultQ)\n\t}\n\n\tset_hiddenvalues(tw.q, tw.term)\n}\n"],
-  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAKA,eAAsBA,YAAW,MAAM;AACtC,SAAO,WAAsB,IAAI;AAClC;AAEA,eAAsB,OAAO,IAAW,UAAoB,WAAwB,MAAM;AACzF,MAAI,OAAO,GAAG,SAAS;AAAU,UAAM;AACvC,MAAI,CAAC,GAAG,KAAK,MAAM,CAAC,GAAG,KAAK;AAAM,UAAM;AACxC,MAAI,CAAC,GAAG,KAAK,OAAO,CAAC,OAAO,UAAU,GAAG,KAAK,KAAK,KAAK,CAAC,OAAO,UAAU,GAAG,KAAK,IAAI;AACrF,UAAM;AACP,MAAI,CAAC,GAAG,KAAK,OAAO,CAAC,GAAG,KAAK;AAAK;AAElC,MAAI,CAAC,OAAO,KAAK,GAAG,CAAC,EAAE,SAAS,MAAM;AAAG,OAAG,EAAE,OAAO;AACrD,MAAI,CAAC,GAAG,KAAK;AAAc,OAAG,KAAK,eAAe,EAAE,UAAU,MAAM;AACpE,MAAI,GAAG,EAAE,QAAQ,uBAAuB;AACvC,QAAI,CAAC,OAAO,UAAU,GAAG,EAAE,uBAAuB;AAAG,YAAM;AAAA,EAC5D;AACA,MAAI,GAAG,EAAE,QAAQ,mBAAmB;AACnC,QAAI,CAAC,GAAG,EAAE;AAAW,YAAM;AAAA,EAC5B;AAEA,MAAI,UAAU;AAEb,cAAU,GAAG,GAAG,QAAQ;AAAA,EACzB;AAEA,mBAAiB,GAAG,GAAG,GAAG,IAAI;AAC/B;",
-  "names": ["getHandler"]
-}

package/dist/snplocus-L6IAD5O2.js

@@ -1,237 +0,0 @@
-import {
-  filterInit,
-  getNormalRoot
-} from "./chunk-2HB765M6.js";
-import {
-  makeSnpSelect,
-  mayRestrictAncestry
-} from "./chunk-JS4PIGRN.js";
-import "./chunk-ZQN7RJDL.js";
-import "./chunk-L6PTW3VL.js";
-import "./chunk-3EAPD7JJ.js";
-import "./chunk-B2WJXDDI.js";
-import "./chunk-EY7JFZ4D.js";
-import "./chunk-CLHA5AEH.js";
-import "./chunk-252GVCUB.js";
-import "./chunk-7KFEDC2T.js";
-import {
-  addGeneSearchbox
-} from "./chunk-A3GQXDSC.js";
-import "./chunk-6XR2LO7D.js";
-import "./chunk-FZXMYGIE.js";
-import "./chunk-PWTXVCZ4.js";
-import "./chunk-FCPSU6WB.js";
-import "./chunk-O32YEJMI.js";
-import "./chunk-FOSTUUJG.js";
-import "./chunk-PGCZMKZL.js";
-import "./chunk-EG3MKQQH.js";
-import "./chunk-L7QWRU5Z.js";
-import "./chunk-JVUJSWZ2.js";
-import "./chunk-JV3G5Q3X.js";
-import "./chunk-ALPXXDQD.js";
-import "./chunk-CTQFEFIV.js";
-import "./chunk-RKJGIOIF.js";
-import "./chunk-P64DWRTC.js";
-import "./chunk-ROQ5WSLC.js";
-import "./chunk-452UVSLH.js";
-import "./chunk-7YY2KB6H.js";
-import "./chunk-2BM5YZ6X.js";
-import "./chunk-WFANY24Z.js";
-import "./chunk-BT2NCQ7T.js";
-import "./chunk-XNPZE2WZ.js";
-import "./chunk-WMK7VUYQ.js";
-import "./chunk-ZRUQHHLI.js";
-import "./chunk-JASS6SUY.js";
-import "./chunk-NUYFQ7WK.js";
-import "./chunk-P7BTNMOS.js";
-import "./chunk-5IJCZCP7.js";
-import "./chunk-CKF26VJ7.js";
-import "./chunk-Y6SKTI7D.js";
-import "./chunk-F3OQE4AZ.js";
-
-// termsetting/handlers/snplocus.ts
-var term_name = "Variants in a locus";
-function getHandler(self) {
-  return {
-    getPillName() {
-      return self.term.name;
-    },
-    getPillStatus() {
-      if (!self.term || !self.q)
-        return;
-      if (!self.term.snps)
-        throw `Missing term.snps [snplocs.ts getPillStatus()]`;
-      let text = `${self.q.chr}:${self.q.start}-${self.q.stop}, ${self.term.snps.length} variant${self.term.snps.length > 1 ? "s" : ""}`;
-      if (self.term.reachedVariantLimit) {
-        text += '<span style="margin-left: 6px; background:#aaa; font-size:1em;font-style: normal; border-radius: 7px;color:white;padding:0px 5px;">&#9888;<span>';
-      }
-      return { text };
-    },
-    validateQ(data) {
-      validateQ(data);
-    },
-    async showEditMenu(div) {
-      await makeEditMenu(self, div);
-    }
-    /* no need for postMain()
-    cache file contains all samples,
-    variants in a cache file is only determined by locus range and info fields
-    thus no need to regenerate cache file upon subcohort or filter change via pill.main()
-    async postMain() {
-    	if (self.q && self.q.chr) {
-    		await validateInput(self)
-    	}
-    }
-    */
-  };
-}
-async function makeEditMenu(self, div0) {
-  const div = div0.append("div").style("margin", "15px");
-  const select_ancestry = await mayRestrictAncestry(self, div);
-  const coordResult = addGeneSearchbox({
-    genome: self.opts.genomeObj,
-    tip: self.dom.tip2,
-    row: div.append("div").style("margin-top", "20px"),
-    defaultCoord: self.q && self.q.chr ? { chr: self.q.chr, start: self.q.start, stop: self.q.stop } : void 0
-  });
-  div.select(".sja_genesearchinput").style("margin", "0px");
-  div.append("span").style("margin", "5px 0px").style("display", "inline-block").style("opacity", 0.4).style("font-size", ".7em").html(
-    '"Gene": Gene name (e.g. AKT1)</br>"Position": chr:start-stop (e.g. chr1:5000-6000)</br>"dbSNP": dbSNP accession (e.g. rs1042522)'
-  );
-  await mayDisplayVariantFilter(self, self.q?.variant_filter, div);
-  const [input_AFcutoff, select_alleleType, select_geneticModel] = makeSnpSelect(
-    div.append("div").attr("class", "sjpp-snp-select").style("margin-top", "15px"),
-    self,
-    "snplocus"
-  );
-  if (self.usecase.target == "dataDownload")
-    div.select(".sjpp-snp-select").style("display", "none");
-  const btnRow = div.append("div").style("margin-top", "15px");
-  btnRow.append("button").style("margin-top", "15px").text("Submit").on("click", async (event) => {
-    if (!coordResult.chr)
-      return window.alert("Invalid coordinate");
-    event.target.disabled = true;
-    event.target.innerHTML = "Validating input...";
-    if (self.term) {
-    } else {
-      self.term = { id: makeId() };
-    }
-    if (!self.q)
-      self.q = {};
-    self.term.type = "snplocus";
-    self.q.chr = coordResult.chr;
-    self.q.start = coordResult.start;
-    self.q.stop = coordResult.stop;
-    self.term.name = term_name;
-    delete self.term.snps;
-    self.q.variant_filter = getNormalRoot(self.variantFilter.active);
-    await validateInput(self);
-    {
-      const v = Number(input_AFcutoff.property("value"));
-      self.q.AFcutoff = v < 0 || v >= 100 ? 5 : v;
-    }
-    self.q.alleleType = select_alleleType.property("selectedIndex");
-    self.q.geneticModel = select_geneticModel.property("selectedIndex");
-    if (select_ancestry) {
-      self.q.restrictAncestry = select_ancestry.node().options[select_ancestry.property("selectedIndex")].__ancestry_obj;
-    }
-    self.runCallback();
-  });
-  btnRow.append("span").style("padding-left", "15px").style("opacity", 0.8).style("font-size", ".8em").text(
-    self.usecase.target == "dataDownload" ? "" : "Variants will be treated individually in separate regression models"
-  );
-}
-async function validateInput(self) {
-  const data = await self.vocabApi.validateSnps(self.q);
-  if (data.error)
-    throw data.error;
-  self.q.cacheid = data.cacheid;
-  self.term.snps = data.snps;
-  self.term.reachedVariantLimit = data.reachedVariantLimit;
-}
-function validateQ(data) {
-  const q = data.q;
-  if (!Number.isFinite(q.AFcutoff))
-    throw "AFcutoff is not number";
-  if (q.AFcutoff < 0 || q.AFcutoff > 100)
-    throw "AFcutoff is not within 0 to 100";
-  if (![0, 1].includes(q.alleleType))
-    throw "alleleType value is not one of 0/1";
-  if (![0, 1, 2, 3].includes(q.geneticModel))
-    throw "geneticModel value is not one of 0/1";
-  if (!q.chr)
-    throw "chr missing";
-  if (!Number.isInteger(q.start))
-    throw "start coordinate is not integer";
-  if (!Number.isInteger(q.stop))
-    throw "stop coordinate is not integer";
-  if (q.start < 0)
-    throw "start < 0";
-  if (q.stop <= q.start)
-    throw "stop <= start";
-}
-async function fillTW(tw, vocabApi) {
-  try {
-    validateQ(tw);
-  } catch (e) {
-    throw "snplocus validateQ(): " + e;
-  }
-  if (!tw.term.name)
-    tw.term.name = term_name;
-  if (tw.id == void 0 || tw.id == "") {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = makeId();
-    }
-    tw.id = tw.term.id;
-  } else {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = tw.id;
-    }
-  }
-  await validateInput({
-    term: tw.term,
-    q: tw.q,
-    vocabApi
-  });
-}
-function makeId() {
-  return "snplocus" + Math.random();
-}
-async function mayDisplayVariantFilter(self, filterInState, holder, callback2) {
-  if (!self.variantFilter) {
-    self.variantFilter = await self.vocabApi.get_variantFilter();
-  }
-  if (!self.variantFilter.terms) {
-    return;
-  }
-  if (!self.variantFilter.opts)
-    throw "variantFilter.opts{} missing";
-  if (!self.variantFilter.filter)
-    throw ".filter missing from variantFilter{}";
-  if (!Array.isArray(self.variantFilter.terms) || self.variantFilter.terms.length == 0)
-    throw "variantFilter.terms[] is not non-empty array";
-  if (filterInState) {
-    self.variantFilter.active = JSON.parse(JSON.stringify(filterInState));
-  } else {
-    self.variantFilter.active = JSON.parse(JSON.stringify(self.variantFilter.filter));
-  }
-  const div = holder.append("div").style("margin-top", "15px");
-  div.append("span").text("VARIANT FILTERS").style("font-size", ".8em").style("opacity", 0.5);
-  const filterBody = div.append("div");
-  filterInit({
-    joinWith: self.variantFilter.opts.joinWith,
-    emptyLabel: "+Variant Filter",
-    holder: filterBody,
-    vocab: { terms: self.variantFilter.terms },
-    callback: async (filter) => {
-      self.variantFilter.active = filter;
-      if (callback2)
-        await callback2();
-    }
-  }).main(self.variantFilter.active);
-}
-export {
-  fillTW,
-  getHandler
-};
-//# sourceMappingURL=snplocus-L6IAD5O2.js.map