@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/SC-RA46YM57.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/sc/model/SCModel.ts", "../plots/sc/viewModel/SCViewModel.ts", "../plots/sc/interactions/SCInteractions.ts", "../plots/sc/view/PlotSelectionRenderer.ts", "../plots/sc/view/PlotButtons.ts", "../plots/sc/view/SCViewRenderer.ts", "../plots/sc/defaults.ts", "../plots/sc/viewModel/plotData.ts", "../plots/sc/SC.ts"],
-  "sourcesContent": ["import type { AppApi } from '#rx'\nimport type { SCFormattedState } from '../SCTypes'\nimport { dofetch3 } from '#common/dofetch'\n\n/** Fetches data for sc app */\nexport class SCModel {\n\tapp: AppApi\n\tid?: string\n\tstate: SCFormattedState\n\n\tconstructor(app: AppApi, id: string) {\n\t\tthis.app = app\n\t\tthis.id = id\n\t\t//Should only use immutable state attributes (e.g. vocab.genome)\n\t\tthis.state = this.app.getState()\n\t}\n\n\t/********** Single Cell SAMPLES for rendering the table *********/\n\t//The table data does not update\n\t//Should only need to init once\n\tasync getSampleData() {\n\t\tconst body = this.getSampleRequestOpts()\n\t\treturn await dofetch3('termdb/singlecellSamples', { body })\n\t}\n\n\t//May involve more complicated logic later\n\tgetSampleRequestOpts() {\n\t\treturn {\n\t\t\tgenome: this.state.vocab.genome,\n\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\tfilter0: this.state.termfilter.filter0 || null\n\t\t}\n\t}\n\n\t//Fetches optional name for ds defined columns\n\tasync getColumnLabels(dsScSamples: { [key: string]: any }) {\n\t\tif (!dsScSamples || !dsScSamples.sampleColumns) return\n\t\tconst colsCopy = structuredClone(dsScSamples.sampleColumns)\n\t\tfor (const col of colsCopy) {\n\t\t\tlet label = col.termid\n\t\t\ttry {\n\t\t\t\tlabel = (await this.app.vocabApi.getterm(col.termid)).name\n\t\t\t} catch (e: any) {\n\t\t\t\tif (e.message) {\n\t\t\t\t\t//Ignore. if statement to prevent tsc error.\n\t\t\t\t}\n\t\t\t\t/** Ignore errors and use the termid as the column header.\n\t\t\t\t * this is due to practical constrain that gdc needs to supply\n\t\t\t\t * analysis.workflow_type as 'Library', but this is not a term\n\t\t\t\t * in gdc dictionary */\n\t\t\t}\n\t\t\tcol.label = label\n\t\t}\n\t\treturn colsCopy\n\t}\n\n\t/********** Single Cell DATA for rendering plots *********/\n\tasync getData() {\n\t\tconst body = this.getDataRequestOpts()\n\t\tif (!body) return\n\t\treturn await dofetch3('termdb/singlecellData', { body })\n\t}\n\n\tgetDataRequestOpts() {\n\t\tconst state = this.app.getState()\n\t\tconst singleCellTermdbConfig = state.termdbConfig?.queries?.singleCell\n\t\tif (!singleCellTermdbConfig?.data) throw new Error('No singleCell.data defined in termdbConfig.queries')\n\n\t\tconst config = state.plots.find((p: any) => p.id === this.id)\n\t\tif (!config.settings.sc.item) return\n\n\t\t//TODO: May need to only use active plots for this sample\n\t\tconst plots = singleCellTermdbConfig.data.plots.map(p => p.name)\n\n\t\treturn {\n\t\t\tgenome: this.state.vocab.genome,\n\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\tplots,\n\t\t\tsample: {\n\t\t\t\teID: config.settings.sc.item.experiment,\n\t\t\t\tsID: config.settings.sc.item.sample\n\t\t\t}\n\t\t}\n\t}\n}\n", "import type { AppApi } from '#rx'\nimport type { TableColumn, TableRow } from '#dom'\nimport type { SCConfig, SCFormattedState, SampleColumn } from '../SCTypes'\nimport type { SingleCellSample } from '#types'\n\n/** TODOs\n *  - ?Implement data mapper for buttons?\n *  - Implement data mapper for plots in the dashboard\n */\n\n// export type SCViewModelData = {\n// \t//TODO\n// }\n\ntype TableData = {\n\trows: TableRow[]\n\tcolumns: TableColumn[]\n\tselectedRows: number[]\n}\n\nexport class SCViewModel {\n\tapp: AppApi\n\tstate: SCFormattedState\n\ttableData: TableData\n\n\tconstructor(app: AppApi, config: SCConfig, items: SingleCellSample[], sampleColumns?: SampleColumn[]) {\n\t\tthis.app = app\n\t\tthis.state = this.app.getState()\n\n\t\t//Should only be called once\n\t\tconst [rows, columns] = this.getTabelData(config, items, sampleColumns)\n\t\tconst selectedRows: number[] = []\n\t\tconst i = items.findIndex(i => i.sample == config.settings.sc.item?.sample)\n\t\tif (i != -1) selectedRows.push(i)\n\n\t\t/** Returning this data separately from the eventual\n\t\t * viewData because it's static. */\n\t\tthis.tableData = {\n\t\t\trows: rows as any,\n\t\t\tcolumns: columns as any,\n\t\t\tselectedRows\n\t\t}\n\t}\n\n\tgetTabelData(plotConfig: SCConfig, items: SingleCellSample[], sampleColumns?: SampleColumn[]) {\n\t\tconst rows: TableRow[] = []\n\t\tconst hasExperiments = items.some(i => i.experiments)\n\n\t\t// first column is sample and is hardcoded\n\t\tconst columns: TableColumn[] = [{ label: plotConfig.settings.sc.columns.sample, sortable: true }]\n\t\tif (hasExperiments) columns.push({ label: 'Sample', sortable: true }) //add after the case column\n\n\t\t// add in optional sample columns\n\t\tfor (const col of sampleColumns || []) {\n\t\t\tcolumns.push({\n\t\t\t\tlabel: col.label,\n\t\t\t\twidth: '14vw',\n\t\t\t\tsortable: true\n\t\t\t})\n\t\t}\n\n\t\t// if samples are using experiments, add the hardcoded experiment column at the end\n\t\tif (hasExperiments) columns.push({ label: 'Experiment', sortable: true }) // corresponds to this.samples[].experiments[].experimentID\n\n\t\tfor (const item of items) {\n\t\t\tif (hasExperiments)\n\t\t\t\t//GDC\n\t\t\t\tfor (const exp of item.experiments!) {\n\t\t\t\t\t// first cell is always sample name. sneak in experiment object to be accessed in click callback\n\t\t\t\t\t//TODO: Consider removing the experimentID as it is no longer needed.\n\t\t\t\t\tconst row: { [index: string]: any }[] = [{ value: item.sample, __experimentID: exp.experimentID }]\n\t\t\t\t\t// hardcode to expect exp.sampleName and add this as a column\n\t\t\t\t\trow.push({ value: exp.sampleName })\n\t\t\t\t\t// optional sample and experiment columns\n\t\t\t\t\tfor (const col of sampleColumns || []) {\n\t\t\t\t\t\trow.push({ value: item[col.termid] })\n\t\t\t\t\t}\n\n\t\t\t\t\t// hardcode to always add in experiment id column\n\t\t\t\t\tif (this.state.vocab.dslabel == 'GDC')\n\t\t\t\t\t\trow.push({ value: exp.experimentID, url: `https://portal.gdc.cancer.gov/files/${exp.experimentID}` })\n\t\t\t\t\telse row.push({ value: exp.experimentID })\n\t\t\t\t\trows.push(row)\n\t\t\t\t}\n\t\t\telse {\n\t\t\t\t// sample does not use experiment\n\t\t\t\t// first cell is sample name\n\t\t\t\tconst row: { [index: string]: any }[] = [{ value: item.sample }]\n\t\t\t\t// optional sample columns\n\t\t\t\tfor (const col of sampleColumns || []) {\n\t\t\t\t\trow.push({ value: item[col.termid] })\n\t\t\t\t}\n\t\t\t\trows.push(row)\n\t\t\t}\n\t\t}\n\t\treturn [rows, columns]\n\t}\n}\n", "import type { AppApi } from '#rx'\n\n/** Handles the interactivity from the view */\nexport class SCInteractions {\n\tapp: AppApi\n\tdom: any //May not be necessary\n\tid: string\n\tgetState: () => any\n\n\tconstructor(app: AppApi, dom: any, id: string, getState: () => any) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t\tthis.getState = getState()\n\t}\n\n\t/** Used in the gene search menu shown on click from a plot btn\n\t * Add the plot to the state.plots array with .parentId. Adding\n\t * .parentId prevents the plot from launching in a new sandbox.\n\t * Pass the .parentId to both the plotConfig and the action.\n\t * this.getState() in SC.ts will find all the subplots with the parentId==this.id\n\t * SC.main() initializes the subplots as components in chartsDiv\n\t */\n\tasync createSubplot(config) {\n\t\tconst item = this.app.getState().plots.find(p => p.id === this.id)?.settings.sc.item\n\t\t//'item' isFrozen. Pass the clone to avoid downstream issues.\n\t\tconst c = Object.assign({}, config, { parentId: this.id, scItem: structuredClone(item) })\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tparentId: this.id,\n\t\t\tconfig: c\n\t\t})\n\t}\n\n\t/** Updates the item in the plot settings */\n\tasync updateItem(item) {\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { settings: { sc: { item } } }\n\t\t})\n\t}\n\n\ttoggleLoading(on: boolean) {\n\t\tif (on) {\n\t\t\tthis.dom.loading.selectAll('*').remove()\n\t\t\tthis.dom.loading\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('top', '50%')\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sjpp-spinner')\n\t\t\tthis.dom.loading.style('display', '')\n\t\t} else {\n\t\t\tthis.dom.loading.selectAll('.sjpp-spinner').remove()\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t}\n\t}\n}\n", "import type { SCDom, SCTableData } from '../SCTypes'\nimport type { TableCell } from '#dom'\nimport { renderTable } from '#dom'\nimport type { SCInteractions } from '../interactions/SCInteractions'\n\nexport class PlotSelectionRenderer {\n\tdom: SCDom\n\tinteractions: SCInteractions\n\n\tconstructor(dom: SCDom, interactions: SCInteractions, tableData: SCTableData) {\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.renderSamplesTable(tableData)\n\t}\n\n\t/** Users select one item at a time to render the plot buttons\n\t * to init() plots in the dashboard.*/\n\trenderSamplesTable(tableData: SCTableData) {\n\t\trenderTable({\n\t\t\trows: tableData.rows,\n\t\t\tcolumns: tableData.columns,\n\t\t\tdiv: this.dom.tableDiv,\n\t\t\tsingleMode: true,\n\t\t\tmaxWidth: tableData.columns.length > 3 ? '98vw' : '40vw',\n\t\t\tmaxHeight: '30vh',\n\t\t\theader: {\n\t\t\t\tallowSort: true,\n\t\t\t\tstyle: { 'text-transform': 'capitalize' }\n\t\t\t},\n\t\t\tstriped: true,\n\t\t\tselectedRows: tableData.selectedRows,\n\t\t\tnoButtonCallback: index => {\n\t\t\t\tconst item = {}\n\t\t\t\ttableData.rows[index].forEach((r: TableCell, idx: number) => {\n\t\t\t\t\tif (!r.value) return\n\t\t\t\t\titem[tableData.columns[idx].label.toLowerCase()] = r.value\n\t\t\t\t})\n\t\t\t\tthis.interactions.updateItem(item)\n\t\t\t\tthis.dom.plotsBtnsDiv.style('display', 'block')\n\t\t\t}\n\t\t})\n\t}\n}\n", "import type { Div, Elem } from '../../../types/d3'\nimport type { SCInteractions } from '../interactions/SCInteractions'\nimport { Menu, GeneSetEditUI } from '#dom'\nimport { digestMessage } from '#termsetting'\nimport { SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION, TermTypeGroups } from '#shared/terms.js'\n\n/** Rendering for the plot buttons that appear below the item\n * table.\n *\n * Notes:\n *  - The hierarchical clustering limits to the first 100 genes.\n *\n ******* TODOs:\n * - Implement ds specific keys or logic for item name\n * - Update anywhere with 'CHANGEME' before prod\n * - Disable all plot btns until plot loads for performance??\n *\n ******* Scatter plot implementation TODOs:\n * - Check that the proper single cell data is used\n * - Configure tooltip to use 'cell' and not 'sample'\n * - term2 in the config is currently defined in\n * queries.singlecell.data.plots.[i].colorColumns. Need to:\n * 1. change that dataset obj and\n * 2. use new obj in the config\n *\n ******* Hier clustering implenentation TODOs and questions:\n * The matrix ** does not ** properly pull single cell data yet.\n * This implementation works as a placeholder for now.\n * Need to revisit before production.\n *\n * Questions:\n * - Limit to 100 genes or no?\n * - What settings to use for hier cluster?\n * */\nexport class PlotButtons {\n\tplotBtnsDom: {\n\t\tpromptDiv: Div\n\t\tselectPrompt: Elem\n\t\tbtnsDiv: Div\n\t\ttip: Menu\n\t}\n\tdata?: any\n\titem?: { [key: string]: any }\n\tinteractions: SCInteractions\n\tscTermdbConfig: any\n\tsettings?: any\n\tscctTerms?: any[]\n\n\tconstructor(interactions: SCInteractions, holder: Div) {\n\t\tholder.style('padding', '10px')\n\t\tconst promptDiv = holder.append('div').style('padding', '10px 0').text('Select data from')\n\t\tthis.plotBtnsDom = {\n\t\t\tpromptDiv,\n\t\t\tselectPrompt: promptDiv.append('span'),\n\t\t\tbtnsDiv: holder.append('div'),\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t\tthis.interactions = interactions\n\t\tconst state = this.interactions.getState as any\n\t\tthis.scctTerms = state.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE]\n\t\tthis.scTermdbConfig = state.termdbConfig.queries.singleCell\n\t}\n\n\tupdate(settings, data) {\n\t\t/** If the user has not selected a item yet but clicks\n\t\t * the select item/plots btn above the table, the prompt appears\n\t\t * unnecessarily */\n\t\tconst item = settings.sc.item\n\t\tthis.plotBtnsDom.promptDiv.style('display', !item ? 'none' : 'block')\n\t\tif (!item) return\n\t\tif (data != null && data.plots) this.data = data\n\t\tthis.settings = settings\n\t\tthis.item = item\n\t\tconst name = item.sample // add ds specific keys/logic here\n\t\tthis.plotBtnsDom.selectPrompt.text(` ${name}:`)\n\t\tthis.renderChartBtns()\n\t}\n\n\trenderChartBtns() {\n\t\tthis.plotBtnsDom.btnsDiv.selectAll('*').remove()\n\t\tconst btns = this.getChartBtnOpts()\n\n\t\tthis.plotBtnsDom.btnsDiv\n\t\t\t.selectAll('button')\n\t\t\t.data(btns.filter(b => b.isVisible()))\n\t\t\t.enter()\n\t\t\t.append('button')\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('border-color', 'transparent')\n\t\t\t.style('background-color', '#CFE2F3')\n\t\t\t.style('margin', '0 10px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.text(b => b.label)\n\t\t\t.on('click', async (e, plot) => {\n\t\t\t\tif (plot.open) {\n\t\t\t\t\tthis.plotBtnsDom.tip.clear().showunder(e.target)\n\t\t\t\t\tplot.open(plot, this)\n\t\t\t\t} else {\n\t\t\t\t\tconst config = await plot.getPlotConfig()\n\t\t\t\t\tawait this.interactions.createSubplot(config)\n\t\t\t\t}\n\t\t\t})\n\t}\n\tgetChartBtnOpts() {\n\t\tconst btns: {\n\t\t\tlabel: string\n\t\t\tisVisible: () => boolean\n\t\t\topen?: (plot: any, self: PlotButtons) => void\n\t\t\tgetPlotConfig: (f?: any, g?: any) => any\n\t\t}[] = []\n\n\t\tfor (const plots of this.scTermdbConfig?.data?.plots || []) {\n\t\t\tbtns.push({\n\t\t\t\tlabel: plots.name,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tgetPlotConfig: async () => {\n\t\t\t\t\treturn await this.getSingleCellConfig(plots.name)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tbtns.push(\n\t\t\t{\n\t\t\t\tlabel: 'Gene expression',\n\t\t\t\tisVisible: () => true,\n\t\t\t\topen: this.geneSearchMenu,\n\t\t\t\tgetPlotConfig: async geneLst => {\n\t\t\t\t\tif (!geneLst.length) {\n\t\t\t\t\t\talert('No genes selected to launch gene expression subplot [PlotButtons.ts getChartBtnOpts()]')\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\t/** If 1 gene, launch violin\n\t\t\t\t\t * If 2 genes, launch scatter\n\t\t\t\t\t * If >2 genes, launch hier clustering */\n\t\t\t\t\tif (geneLst.length == 1) return await this.getViolinConfig(geneLst[0].gene)\n\t\t\t\t\telse if (geneLst.length == 2) return await this.getScatterConfig(geneLst)\n\t\t\t\t\telse return this.getClusteringConfig(geneLst)\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Differential expression',\n\t\t\t\tisVisible: () => this.scTermdbConfig.DEgenes,\n\t\t\t\topen: this.termDropdownMenu,\n\t\t\t\tgetPlotConfig: value => {\n\t\t\t\t\t//TODO: refine this config\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchartType: 'differentialAnalysis',\n\t\t\t\t\t\ttermType: SINGLECELL_CELLTYPE,\n\t\t\t\t\t\t//Eventually category will be updated to a term\n\t\t\t\t\t\t// term: {\n\t\t\t\t\t\t// \tname: term\n\t\t\t\t\t\t// },\n\t\t\t\t\t\tcategoryName: `${value}`,\n\t\t\t\t\t\ttermId: this.data.plots[0].colorBy || 'Cluster', //CHANGEME\n\t\t\t\t\t\tsample: this.item!.experiment || this.item!.sample\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t)\n\t\treturn btns\n\t}\n\n\t//********** Btn Menus **********/\n\tgeneSearchMenu(plot: any, self: PlotButtons) {\n\t\tself.plotBtnsDom.tip.clear()\n\n\t\tnew GeneSetEditUI({\n\t\t\tholder: self.plotBtnsDom.tip.d.append('div') as any,\n\t\t\tgenome: self.interactions.app.opts.genome,\n\t\t\tvocabApi: {},\n\t\t\tcallback: async result => {\n\t\t\t\tself.plotBtnsDom.tip.hide()\n\t\t\t\tconst config = await plot.getPlotConfig(result.geneList)\n\t\t\t\tawait self.interactions.createSubplot(config)\n\t\t\t}\n\t\t})\n\t}\n\n\t/** CHANGEME: This elem is a placeholder for now\n\t * Ideally this will call the tree with singleCellCellTerms.\n\t * That term type is not implemented yet. Once it is,\n\t * refactor this workflow to use the tree. */\n\ttermDropdownMenu(plot: any, self: PlotButtons) {\n\t\t//CHANGEME: This ds obj needs to be defined as a term, not column name\n\t\tself.plotBtnsDom.tip.clear()\n\t\tconst _plot = self.data.plots[0]\n\n\t\tconst wrapper = self.plotBtnsDom.tip.d.append('div').style('padding', '10px')\n\n\t\twrapper\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.style('width', '300px')\n\t\t\t.text(`View differentially expressed genes of a ${_plot.colorBy.toLowerCase()} versus rest of the cells:`)\n\n\t\tconst select = wrapper\n\t\t\t.append('select')\n\t\t\t.style('margin', '10px 0')\n\t\t\t.style('width', 'auto')\n\t\t\t.style('padding', '5px')\n\t\t\t.on('change', async function () {\n\t\t\t\tself.plotBtnsDom.tip.hide()\n\t\t\t\tconst value = select.node()!.value\n\t\t\t\tif (value.indexOf('Select') == 0) return //ignore prompt option\n\t\t\t\tconst config = plot.getPlotConfig(value, _plot.colorBy)\n\t\t\t\tawait self.interactions.createSubplot(config)\n\t\t\t})\n\n\t\tconst regex = new RegExp(_plot.colorBy, 'g')\n\t\t_plot.clusters.unshift(`Select ${_plot.colorBy}...`)\n\t\tfor (const cluster of _plot.clusters) {\n\t\t\tselect.append('option').attr('value', cluster.replace(regex, '').trim()).text(cluster)\n\t\t}\n\t}\n\n\t//********** Plot Config Helpers **********/\n\tasync getViolinConfig(gene): Promise<object> {\n\t\tif (!this.item) throw new Error('No item selected')\n\t\treturn {\n\t\t\tchartType: 'violin',\n\t\t\tterm: {\n\t\t\t\t$id: await digestMessage(`${gene}-${this.item.sample}-${this.item.experiment}`),\n\t\t\t\tterm: {\n\t\t\t\t\ttype: SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\tid: gene,\n\t\t\t\t\tgene,\n\t\t\t\t\tname: gene,\n\t\t\t\t\tsample: {\n\t\t\t\t\t\tsID: this.item.sample,\n\t\t\t\t\t\teID: this.item.experiment\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t// term2: await this.makeScctTW(this.item, this.scTermdbConfig.data.plots[0])\n\t\t\tterm2: {\n\t\t\t\t//CHANGE ME\n\t\t\t\t$id: await digestMessage(`CHANGEME-${this.item.sample}-${this.item.experiment}`),\n\t\t\t\tterm: {\n\t\t\t\t\ttype: SINGLECELL_CELLTYPE,\n\t\t\t\t\tid: 'cluster', //CHANGE ME, singlecell.data.plots.[i].colorColumns\n\t\t\t\t\tname: 'cluster', //CHANGE ME\n\t\t\t\t\tsample: {\n\t\t\t\t\t\tsID: this.item.sample,\n\t\t\t\t\t\teID: this.item.experiment\n\t\t\t\t\t},\n\t\t\t\t\tplot: 'UMAP' //CHANGEME\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tasync getScatterConfig(geneLst): Promise<object> {\n\t\tif (!this.item) throw new Error('No item selected')\n\t\tconst gene1 = geneLst[0].gene\n\t\tconst gene2 = geneLst[1].gene\n\n\t\treturn {\n\t\t\tchartType: 'sampleScatter',\n\t\t\tterm: {\n\t\t\t\t$id: await digestMessage(`${gene1}-${this.item.sample}-${this.item.experiment}`),\n\t\t\t\tterm: {\n\t\t\t\t\ttype: SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\tgene: gene1,\n\t\t\t\t\tid: gene1,\n\t\t\t\t\tname: gene1,\n\t\t\t\t\tsample: {\n\t\t\t\t\t\tsID: this.item.sample,\n\t\t\t\t\t\teID: this.item.experiment\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tq: { mode: 'continuous' }\n\t\t\t},\n\t\t\tterm2: {\n\t\t\t\t$id: await digestMessage(`${gene2}-${this.item.sample}-${this.item.experiment}`),\n\t\t\t\tterm: {\n\t\t\t\t\ttype: SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\tgene: gene2,\n\t\t\t\t\tid: gene2,\n\t\t\t\t\tname: gene2,\n\t\t\t\t\tsample: {\n\t\t\t\t\t\tsID: this.item.sample,\n\t\t\t\t\t\teID: this.item.experiment\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tq: { mode: 'continuous' }\n\t\t\t}\n\t\t}\n\t}\n\n\tgetClusteringConfig(geneLst): object {\n\t\tif (!this.item) throw new Error('No item selected')\n\t\t//limit to 100 genes for performance\n\t\tconst tws = geneLst.slice(0, 100).map(g => {\n\t\t\treturn {\n\t\t\t\tterm: {\n\t\t\t\t\tgene: g.gene,\n\t\t\t\t\tname: `${g.gene} ${this.settings.hierCluster.unit}`,\n\t\t\t\t\ttype: SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\tsample: this.item\n\t\t\t\t},\n\t\t\t\tq: {}\n\t\t\t}\n\t\t})\n\n\t\treturn {\n\t\t\tchartType: 'hierCluster',\n\t\t\ttermgroups: [{ lst: tws, type: 'hierCluster' }],\n\t\t\tdataType: 'geneExpression',\n\t\t\tsettings: { hierCluster: this.settings.hierCluster }\n\t\t}\n\t}\n\n\tasync getSingleCellConfig(plotName): Promise<object> {\n\t\tif (!this.item) throw new Error('No item selected')\n\t\tconst plot = this.scTermdbConfig.data.plots.find(p => p.name == plotName)\n\t\tif (!plot) throw new Error(`No plot by name ${plotName} in data.plots [PlotButtons.ts getSingleCellConfig()]`)\n\t\tconst config: any = {\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsingleCellPlot: {\n\t\t\t\tname: plotName,\n\t\t\t\tsample: {\n\t\t\t\t\tsID: this.item.sample,\n\t\t\t\t\teID: this.item.experiment\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (plot.colorColumns?.[0]) {\n\t\t\t// apply optional color term. hardcodes to 1st of the array\n\t\t\tconfig.colorTW = await this.makeScctTW(this.item, plot)\n\t\t}\n\t\treturn config\n\t}\n\n\t// Quick fix. Eventually use the handler to get the proper term from the termdbConfig\n\tasync makeScctTW(item, plot) {\n\t\tconst colorColName = plot.colorColumns[0].name\n\t\tconst savedTerm = this.scctTerms?.find(t => t.name == colorColName && t.plot == plot.name)\n\t\tif (!savedTerm)\n\t\t\tthrow new Error(\n\t\t\t\t`No term found for colorColumn=${colorColName} in .termType2terms.[TermTypeGroups.SINGLECELL_CELLTYPE] for plot ${plot.name}`\n\t\t\t)\n\t\tconst term = Object.assign(structuredClone(savedTerm), {\n\t\t\tsample: {\n\t\t\t\tsID: item.sample,\n\t\t\t\teID: item.experiment\n\t\t\t}\n\t\t})\n\t\tconst id = await digestMessage(`${plot.name}-${item.sample}-${item.experiment}`)\n\t\treturn Object.assign({ $id: id }, { term })\n\t}\n}\n", "import type { SCDom, Segments } from '../SCTypes'\nimport type { SCInteractions } from '../interactions/SCInteractions'\nimport { PlotSelectionRenderer } from './PlotSelectionRenderer'\nimport { PlotButtons } from './PlotButtons'\n\nexport class SCViewRenderer {\n\tdom: SCDom\n\tinteractions: SCInteractions\n\tplotBtns: PlotButtons\n\t//On load, show table\n\t//Eventually maybe an app dispatch and not a flag\n\tstatic inUse = true\n\tsegments: Segments\n\n\tconstructor(dom: SCDom, interactions: SCInteractions, segments: Segments) {\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.plotBtns = new PlotButtons(this.interactions, this.dom.plotsBtnsDiv)\n\t\tthis.segments = segments\n\t}\n\n\trender(tableData) {\n\t\tthis.renderSelectBtn()\n\t\tnew PlotSelectionRenderer(this.dom, this.interactions, tableData)\n\t\tthis.dom.plotsBtnsDiv.style('display', 'none')\n\t}\n\n\t/** Renders the select btn at the top of the page that\n\t * show/hides the item table and plot buttons */\n\trenderSelectBtn() {\n\t\tthis.dom.selectBtnDiv.style('padding', '10px')\n\n\t\tconst btn = this.dom.selectBtnDiv\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-sc-item-table-select-btn')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '5px 10px')\n\t\t\t.style('background-color', 'transparent')\n\t\t\t//Will need to use ds specific keys/logic here\n\t\t\t.text('Select sample and plots')\n\n\t\tconst arrowSpan = btn.append('span').style('font-size', '0.8em').style('padding-left', '3px').text('\u25BC')\n\n\t\tbtn.on('click', () => {\n\t\t\tSCViewRenderer.inUse = !SCViewRenderer.inUse\n\t\t\tarrowSpan.text(SCViewRenderer.inUse ? '\u25BC' : '\u25B2')\n\t\t\tthis.dom.tableDiv.style('display', SCViewRenderer.inUse ? 'block' : 'none')\n\t\t\tthis.dom.plotsBtnsDiv.style('display', SCViewRenderer.inUse ? 'block' : 'none')\n\t\t})\n\t}\n\n\tupdate(settings, data) {\n\t\tthis.plotBtns.update(settings, data)\n\t}\n\n\tremoveSegments() {\n\t\tif (!Object.keys(this.segments).length) return\n\t\tfor (const [key, segment] of Object.entries(this.segments)) {\n\t\t\t//DO NOT use .sjpp-sandbox as the identifier.\n\t\t\t//That div remains after user deletes the plot\n\t\t\tconst plots = segment.subplots.selectAll('.sjpp-output-sandbox-header').size()\n\t\t\tif (!plots) {\n\t\t\t\tsegment.title.remove()\n\t\t\t\tsegment.subplots.remove()\n\t\t\t\tdelete this.segments[key]\n\t\t\t}\n\t\t}\n\t}\n}\n", "/** Define all subplot settings here */\nexport function getDefaultSCAppSettings(overrides = {}, app) {\n\tconst defaults = {\n\t\tsc: {\n\t\t\tcolumns: {\n\t\t\t\t// TODO: Implement ds specific column name\n\t\t\t\tsample: 'Sample'\n\t\t\t},\n\t\t\titem: undefined\n\t\t},\n\t\thierCluster: {\n\t\t\tunit: app.vocabApi.termdbConfig.queries.geneExpression?.unit || 'Gene Expression',\n\t\t\tyDendrogramHeight: 0,\n\t\t\tclusterSamples: false\n\t\t}\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n", "export default function formatPlotData(_plots) {\n\tconst plots = structuredClone(_plots)\n\n\tfor (const plot of plots) {\n\t\tconst expCells = plot.expCells.sort((a, b) => a.geneExp - b.geneExp)\n\t\tplot.cells = [...plot.noExpCells, ...expCells]\n\t\tconst clusters = new Set(plot.cells.map(c => c.category))\n\n\t\tplot.clusters = Array.from(clusters).sort((a: any, b: any) => {\n\t\t\tconst num1 = parseInt(a.split(' ')[1])\n\t\t\tconst num2 = parseInt(b.split(' ')[1])\n\t\t\treturn num1 - num2\n\t\t})\n\t}\n\treturn plots\n}\n", "import type { BasePlotConfig, MassAppApi, MassState } from '#mass/types/mass'\nimport type { SCConfigOpts, SCDom, SCFormattedState, SCViewerOpts, SampleColumn, Segments } from './SCTypes'\nimport type { SingleCellSample } from '#types'\nimport { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { SCModel } from './model/SCModel'\nimport { SCViewModel } from './viewModel/SCViewModel'\nimport { SCInteractions } from './interactions/SCInteractions'\nimport { SCViewRenderer } from './view/SCViewRenderer'\nimport { getDefaultSCAppSettings } from './defaults'\nimport { importPlot } from '#plots/importPlot.js'\nimport { newSandboxDiv } from '#dom'\nimport formatPlotData from './viewModel/plotData.ts'\n\n/** Overall app TODOs:\n *  - Plot buttons\n *  \t- Implement additional menus to appear on click\n *  - Fix any outdated properties in the dataset queries.singleCell obj\n *  - Type all files\n *  - instead of using 'sample', change to 'key' or 'item' or something\n */\n\nclass SCViewer extends PlotBase implements RxComponent {\n\tstatic type = 'sc'\n\n\ttype: string\n\tcomponents: { plots: { [key: string]: any } }\n\tdom: SCDom\n\tinteractions?: SCInteractions\n\titems?: SingleCellSample[]\n\titemColumns?: SampleColumn[]\n\tmodel?: SCModel\n\tsegments: Segments\n\tview?: SCViewRenderer\n\tviewModel?: SCViewModel\n\n\tconstructor(opts: SCViewerOpts, api: any) {\n\t\tsuper(opts, api)\n\t\tthis.type = SCViewer.type\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t\tconst div = opts.holder\n\t\t\t.classed('sjpp-sc-main', true)\n\t\t\t.append('div')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\n\t\tthis.dom = {\n\t\t\tdiv,\n\t\t\tloading: opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-sc-loading')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('top', '0')\n\t\t\t\t.style('left', '0')\n\t\t\t\t.style('width', '100%')\n\t\t\t\t.style('height', '100%')\n\t\t\t\t.style('background-color', 'rgba(255, 255, 255, 0.95)')\n\t\t\t\t.style('text-align', 'center'),\n\t\t\tselectBtnDiv: div.append('div').attr('id', 'sjpp-sc-select-btn'),\n\t\t\ttableDiv: div.append('div').attr('id', 'sjpp-sc-item-table'),\n\t\t\tplotsBtnsDiv: div.append('div').attr('id', 'sjpp-sc-plot-buttons').style('display', 'none')\n\t\t}\n\n\t\tthis.segments = {}\n\n\t\t//opts.header is the sandbox header\n\t\tif (opts.header) opts.header.html(`SINGLE CELL`).style('font-size', '0.9em')\n\t}\n\n\tgetState(appState: any): SCFormattedState {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\treturn {\n\t\t\tconfig,\n\t\t\tsubplots: appState.plots.filter(p => p.parentId === this.id),\n\t\t\ttermfilter: appState.termfilter,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\tasync init(appState: MassState) {\n\t\tconst state = this.getState(appState) as SCFormattedState\n\t\t/** ds defines defaults in termdbConfig.queries.singleCell\n\t\t * see Dataset type when resuming development */\n\t\tconst dsScSamples = state.termdbConfig.queries?.singleCell?.samples\n\t\tthis.model = new SCModel(this.app, this.id)\n\t\ttry {\n\t\t\t/** Fetches the single cell sample data for the table */\n\t\t\tconst response = await this.model.getSampleData()\n\t\t\tif (response.error || !response.samples || !response.samples.length) {\n\t\t\t\tthis.app.printError('No samples found for this dataset')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.items = response.samples\n\t\t\tthis.itemColumns = await this.model.getColumnLabels(dsScSamples)\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(`${e.message || e} [SC init()]`)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tthrow new Error(e.message || e)\n\t\t}\n\t\tthis.interactions = new SCInteractions(this.app, this.dom, this.id, () => this.getState(this.app.getState()))\n\t\t//Init view model and view\n\t\tthis.viewModel = new SCViewModel(this.app, state.config, this.items!, this.itemColumns)\n\t\tthis.view = new SCViewRenderer(this.dom, this.interactions, this.segments)\n\n\t\t/** The item data and table rendering should only occur once\n\t\t * .update() in main() handles changes to the buttons and plots */\n\t\tthis.view.render(this.viewModel.tableData)\n\t}\n\n\t//TODO: .text() should be ds specific\n\tasync initSegment(item) {\n\t\tconst caseText = item.case ? `Case: ${item.case}` : ''\n\t\tconst itemText = item.sample ? `Sample: ${item.sample}` : '' //item.cell, etc.\n\t\tconst projectText = item['project id'] ? `Project: ${item['project id']}` : ''\n\t\tconst headerText = [itemText, caseText, projectText].join(' ')\n\n\t\tthis.segments[item.sample] = {\n\t\t\ttitle: this.dom.div\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.style('font-weight', 600)\n\t\t\t\t.text(headerText),\n\t\t\tsubplots: this.dom.div.append('div').style('margin-left', '10px')\n\t\t}\n\t}\n\n\t/** The plot obj is already in state.plots[] but not rendered\n\t * (see SCInteractions). This creates the component and renders the plot */\n\tasync initSubplotComponent(subplot: any) {\n\t\tconst sandbox = newSandboxDiv(this.segments[subplot.scItem.sample].subplots as any, {\n\t\t\tclose: () => {\n\t\t\t\t//Delete the component before calling dispatch\n\t\t\t\t//Prevents main attempting to re-init the component\n\t\t\t\tdelete this.components.plots[subplot.id]\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\tid: subplot.id,\n\t\t\t\t\tparentId: this.id\n\t\t\t\t})\n\t\t\t\t//Could do this in main() but this is more performant\n\t\t\t\tthis.view?.removeSegments()\n\t\t\t},\n\t\t\tplotId: subplot.id,\n\t\t\t// beforePlotId: plot.insertBefore || null,\n\t\t\tstyle: {\n\t\t\t\t//TODO: What width is appropriate here? 50%?\n\t\t\t\twidth: '98.5%'\n\t\t\t}\n\t\t})\n\n\t\tconst opts = Object.assign({}, subplot, {\n\t\t\tapp: this.app,\n\t\t\tholder: sandbox.body,\n\t\t\theader: sandbox.header,\n\t\t\tparentId: this.id,\n\t\t\tid: subplot.id\n\t\t})\n\t\tconst { componentInit } = await importPlot(opts.chartType)\n\t\tthis.components.plots[subplot.id] = await componentInit(opts)\n\t}\n\n\tasync main() {\n\t\tconst state = this.getState(this.app.getState()) as SCFormattedState\n\t\tconst config = state.config\n\n\t\tif (!this.model) throw new Error(`Model not initialized`)\n\t\tif (!this.viewModel) throw new Error(`ViewModel not initialized`)\n\t\tif (!this.view) throw new Error(`View not initialized`)\n\t\tif (!this.interactions) throw new Error(`Interactions not initialized`)\n\n\t\tthis.interactions.toggleLoading(true)\n\n\t\t// const errors = {} collect plot init errors\n\t\tfor (const subplot of state.subplots) {\n\t\t\tif (!this.segments[subplot.scItem.sample]) this.initSegment(subplot.scItem)\n\t\t\tif (!this.components.plots[subplot.id]) await this.initSubplotComponent(subplot)\n\t\t}\n\n\t\tlet data: any = null\n\t\tif (config.settings.sc.item) {\n\t\t\ttry {\n\t\t\t\tdata = await this.model.getData()\n\t\t\t\tif (data.error || !data.plots || !data.plots.length) {\n\t\t\t\t\tthis.interactions.toggleLoading(false)\n\t\t\t\t\tthis.app.printError(data.error)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t} catch (e: any) {\n\t\t\t\tthis.interactions.toggleLoading(false)\n\t\t\t\tif (e instanceof Error) console.error(`${e.message || e} [SC main()]`)\n\t\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\t\tthrow new Error(e.message || e)\n\t\t\t}\n\t\t\tdata.plots = formatPlotData(data.plots)\n\t\t}\n\n\t\tthis.view.update(config.settings, data)\n\t\tthis.interactions.toggleLoading(false)\n\t}\n}\n\nexport const SCInit = getCompInit(SCViewer)\nexport const componentInit = SCInit\n\nexport function getPlotConfig(opts: SCConfigOpts, app: MassAppApi) {\n\tconst config = {\n\t\tchartType: 'sc',\n\t\thidePlotFilter: true,\n\t\tsettings: getDefaultSCAppSettings(opts.overrides, app)\n\t} as any\n\n\treturn copyMerge(config, opts)\n}\n"],
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-}