@sjcrh/proteinpaint-client 2.170.13 → 2.170.16

package/dist/{chunk-HV46AUOB.js → chunk-KCZJDP3N.js}

@@ -3,19 +3,19 @@ import {
 } from "./chunk-ECRSBZLZ.js";
 import {
   hierCluster_interactivity_exports
-} from "./chunk-MW5SFVPY.js";
+} from "./chunk-PYXTLYHY.js";
 import {
   Matrix
-} from "./chunk-H3DCEJBL.js";
+} from "./chunk-MBYRPYP2.js";
 import {
   filterJoin,
   getNormalRoot
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   clusterMethodLst,
   distanceMethodLst,
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   NUMERIC_DICTIONARY_TERM,
   TermTypes2Dt
@@ -253,4 +253,4 @@ export {
   hierClusterInit,
   componentInit
 };
-//# sourceMappingURL=chunk-HV46AUOB.js.map
+//# sourceMappingURL=chunk-KCZJDP3N.js.map

package/dist/{chunk-25MV7QKV.js → chunk-KQQTS2GT.js}

@@ -4,7 +4,7 @@ import {
   filterJoin,
   getFilterItemByTag,
   renderTable
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   TermTypes
 } from "./chunk-YJWWWCJ6.js";
@@ -192,4 +192,4 @@ function getUpdatedQfromClick(plot, term, isHidden = false) {
 export {
   setInteractivity
 };
-//# sourceMappingURL=chunk-25MV7QKV.js.map
+//# sourceMappingURL=chunk-KQQTS2GT.js.map

package/dist/{chunk-X2J3DJX2.js → chunk-LXIL56VX.js}

@@ -1,6 +1,6 @@
 import {
   runproteinpaint
-} from "./chunk-D7QK5NTL.js";
+} from "./chunk-VQD7UONE.js";
 
 // test/front.helpers.js
 var serverData = /* @__PURE__ */ Object.create(null);
@@ -139,4 +139,4 @@ export {
   getRunPp,
   rideInit
 };
-//# sourceMappingURL=chunk-X2J3DJX2.js.map
+//# sourceMappingURL=chunk-LXIL56VX.js.map

package/dist/{chunk-E3IIUVLZ.js → chunk-LYAWTLFE.js}

@@ -1,6 +1,6 @@
 import {
   tkt
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   stratinput
 } from "./chunk-IQIXGTQV.js";
@@ -200,4 +200,4 @@ function check_button4variant(lst) {
 export {
   vcf2dstk
 };
-//# sourceMappingURL=chunk-E3IIUVLZ.js.map
+//# sourceMappingURL=chunk-LYAWTLFE.js.map

package/dist/{chunk-E4KVO2QB.js → chunk-LZDCDSC6.js}

@@ -1,10 +1,10 @@
 import {
   keyupEnter
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   get_bin_label,
   get_bin_range_equation
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 
 // termsetting/handlers/NumCustomBinEditor.ts
 var NumCustomBinEditor = class {
@@ -226,4 +226,4 @@ var NumCustomBinEditor = class {
 export {
   NumCustomBinEditor
 };
-//# sourceMappingURL=chunk-E4KVO2QB.js.map
+//# sourceMappingURL=chunk-LZDCDSC6.js.map

package/dist/{chunk-H3DCEJBL.js → chunk-MBYRPYP2.js}

@@ -1,6 +1,6 @@
 import {
   matrix_layout_exports
-} from "./chunk-QAVBHPY3.js";
+} from "./chunk-BZ2WDV66.js";
 import {
   matrix_serieses_exports
 } from "./chunk-ZSPOCZOT.js";
@@ -12,25 +12,25 @@ import {
 } from "./chunk-NPCN4T5F.js";
 import {
   setComputedConfig
-} from "./chunk-7QW52A66.js";
+} from "./chunk-QWNTXJ7F.js";
 import {
   setMatrixDom
 } from "./chunk-CNBWECUD.js";
 import {
   setInteractivity
-} from "./chunk-FXA25J4U.js";
+} from "./chunk-MO2UD3ZX.js";
 import {
   setRenderers
-} from "./chunk-OIB5C2RK.js";
+} from "./chunk-BAV4MK4A.js";
 import {
   MatrixCluster
 } from "./chunk-A5TSPTYC.js";
 import {
   MatrixControls
-} from "./chunk-GYJW2AB2.js";
+} from "./chunk-RF5NZEPS.js";
 import {
   matrix_data_exports
-} from "./chunk-YIS337R3.js";
+} from "./chunk-5IVHAGW2.js";
 import {
   PlotBase,
   TwRouter,
@@ -38,7 +38,7 @@ import {
   rebaseGroupFilter,
   sayerror,
   svgLegend
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   dt2label,
   mclass,
@@ -482,4 +482,4 @@ export {
   componentInit,
   makeChartBtnMenu
 };
-//# sourceMappingURL=chunk-H3DCEJBL.js.map
+//# sourceMappingURL=chunk-MBYRPYP2.js.map

package/dist/{chunk-VCZZ6N2C.js → chunk-MKFTRLKG.js}

@@ -1,9 +1,9 @@
 import {
   setInteractivity
-} from "./chunk-25MV7QKV.js";
+} from "./chunk-KQQTS2GT.js";
 import {
   setViolinRenderer
-} from "./chunk-U3EF5DDC.js";
+} from "./chunk-3UTJHBNF.js";
 import {
   PlotBase,
   controlsInit,
@@ -13,7 +13,7 @@ import {
   htmlLegend,
   renderTerm1Label,
   term0_term2_defaultQ
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -109,7 +109,10 @@ var ViolinPlot = class extends PlotBase {
         title: controlLabels.term0.title || controlLabels.term0.label,
         label: controlLabels.term0.label,
         vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: this.opts.numericEditMenuVersion,
+        // by default, do not allow continuous mode for divide-by term, since
+        // it will create a separate violin-overlay group per unique float or integer value
+        // and there will nonsensical tens/hundreds of these charts based on the cohort size
+        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
         defaultQ4fillTW: term0_term2_defaultQ
       },
       {
@@ -432,4 +435,4 @@ export {
   getDefaultViolinSettings,
   getPlotConfig
 };
-//# sourceMappingURL=chunk-VCZZ6N2C.js.map
+//# sourceMappingURL=chunk-MKFTRLKG.js.map

package/dist/chunk-MKFTRLKG.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/violin.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge } from '../rx'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from './controls'\nimport setViolinRenderer from './violin.renderer'\n//import htmlLegend from '../dom/html.legend'\nimport { htmlLegend, Menu } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\nimport { setInteractivity } from './violin.interactivity'\nimport { plotColor } from '#shared/common.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\n\n/*\nwhen opts.mode = 'minimal', a minimal violin plot will be rendered that will have a single term and minimal features (i.e. no controls, legend, labels, brushing, transitions, etc.)\n\nTODO default to unit=log if term enables\n*/\n\nclass ViolinPlot extends PlotBase {\n\tstatic type = 'violin'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = 'violin'\n\t}\n\n\tasync init(appState) {\n\t\tconst controls = this.opts.holder.append('div').attr('class', 'sjpp-plot-controls').style('display', 'inline-block')\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', this.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('padding-left', this.opts.mode != 'minimal' ? '20px' : '0px')\n\t\t\t.attr('id', 'sjpp-vp-holder')\n\n\t\tthis.dom = {\n\t\t\thovertip: new Menu({ padding: '3px' }), // separate tips for hover & click on violin labels to avoid interfering\n\t\t\tclicktip: new Menu({ padding: '0px' }),\n\t\t\tsampletabletip: new Menu({ padding: '3px' }), // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..\n\t\t\theader: this.opts.header,\n\t\t\tcontrols,\n\t\t\tbanner: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.style('font-size', '16px'),\n\t\t\tloadingDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', this.opts.mode != 'minimal' ? 'inline-block' : 'none')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.text('Loading ...'),\n\t\t\tviolinDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-violinDiv')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('flex-direction', 'row')\n\t\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t\t.style('max-width', '100vw'),\n\t\t\tlegendDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-vp-legend', true)\n\t\t\t\t.style('margin-left', '-15px')\n\t\t\t\t.style('padding-top', '20px')\n\t\t}\n\n\t\tsetViolinRenderer(this)\n\t\tsetInteractivity(this)\n\n\t\tif (this.opts.mode != 'minimal') {\n\t\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: {}\n\t\t\t})\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tasync setControls() {\n\t\t// do not replace this.components.controls on every re-render,\n\t\t// that could lead to missing control.state if there are errors\n\t\t// with config.terms filling, etc. Better to set getDisplayStyle()\n\t\t// option for an input that doesn't have to be rendered for a given\n\t\t// term/term2/term0 combination.\n\t\tif (this.components.controls) return\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tconst controlLabels = this.state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\tthis.components = {}\n\t\tif (this.opts.mode == 'minimal') return\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term' },\n\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tmenuOptions: 'edit'\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term2',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term2' },\n\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term0',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term0' },\n\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t// by default, do not allow continuous mode for divide-by term, since\n\t\t\t\t// it will create a separate violin-overlay group per unique float or integer value\n\t\t\t\t// and there will nonsensical tens/hundreds of these charts based on the cohort size\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion || ['discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Orientation',\n\t\t\t\ttitle: 'Orientation of the chart',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Data symbol',\n\t\t\t\ttitle: 'Symbol type',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'datasymbol',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Ticks', value: 'rug' },\n\t\t\t\t\t{ label: 'Circles', value: 'bean' },\n\t\t\t\t\t{ label: 'Off', value: 'none' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Scale',\n\t\t\t\ttitle: 'Axis scale',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'unit',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Linear', value: 'abs' },\n\t\t\t\t\t{ label: 'Log10', value: 'log' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Order by',\n\t\t\t\ttitle: 'Order violin plots by parameters',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orderByMedian',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Default', value: false },\n\t\t\t\t\t{ label: 'Median', value: true }\n\t\t\t\t],\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tlet style = 'none'\n\t\t\t\t\tconst charts = this.data?.charts || {}\n\t\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\t\tif (chart?.plots.length > 1) style = ''\n\t\t\t\t\t}\n\t\t\t\t\treturn style\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Symbol size',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'radius',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 30,\n\t\t\t\tmin: 4\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Bins',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'ticks',\n\t\t\t\ttitle: 'Number of bins used to build the plot',\n\t\t\t\tmin: 1,\n\t\t\t\tmax: 50\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: 'Length of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 1000,\n\t\t\t\tmin: 200,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot thickness',\n\t\t\t\ttitle: 'If not specified, the plot thickness is calculated based on the number of categories',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'plotThickness',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 200,\n\t\t\t\tmin: 20,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot padding',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'rowSpace',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 20,\n\t\t\t\tmin: 0,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median length',\n\t\t\t\ttitle: 'Length of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianLength',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 50,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median color',\n\t\t\t\ttitle: 'color of median',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median thickness',\n\t\t\t\ttitle: 'Width of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianThickness',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 10,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 100\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Default violin color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show stats',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showStats',\n\t\t\t\tboxLabel: 'Yes'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show association tests',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showAssociationTests',\n\t\t\t\tboxLabel: 'Yes',\n\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'table-row' : 'none')\n\t\t\t}\n\t\t]\n\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.controls,\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.violin', this.download)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermfilter,\n\t\t\tconfig,\n\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds,\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken()\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tthis.settings = this.config.settings.violin\n\t\tawait this.setControls()\n\n\t\tif (this.config.chartType != this.type && this.config.childType != this.type) return\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(\n\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:1em;margin-left:10px;\">Violin Plot</span>`\n\t\t\t)\n\n\t\t//Fix for rm'ing error message when plot re-renders\n\t\t//Leave in main() so the message doesn't linger whilst\n\t\t//the plot is rendering\n\t\tconst existingMsg = this.dom.banner.style('display', 'none').select('span')\n\t\tif (!existingMsg.empty()) existingMsg.remove()\n\n\t\tconst args = this.validateArgs()\n\t\tlet data\n\t\ttry {\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tdata = await this.app.vocabApi.getViolinPlotData(args, null, this.api.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthrow e\n\t\t}\n\n\t\tthis.data = data\n\t\tif (this.data.error) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthrow this.data.error\n\t\t}\n\t\targs.tw.q.descrStats = this.data.descrStats\n\n\t\tthis.toggleLoadingDiv(this.opts.mode == 'minimal' ? 'none' : '')\n\t\tsetTimeout(\n\t\t\t() => {\n\t\t\t\tthis.render()\n\t\t\t},\n\t\t\tthis.opts.mode == 'minimal' ? 0 : 500\n\t\t)\n\t\tthis.toggleLoadingDiv('none')\n\t}\n\n\tvalidateArgs() {\n\t\tconst { term, term2, term0, settings } = this.config\n\t\tconst s = this.settings\n\t\tconst arg = {\n\t\t\tsvgw: s.svgw,\n\t\t\torientation: s.orientation,\n\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\tdatasymbol: s.datasymbol,\n\t\t\tradius: s.radius,\n\t\t\taxisHeight: s.axisHeight,\n\t\t\trightMargin: s.rightMargin,\n\t\t\tunit: s.unit,\n\t\t\tticks: s.ticks,\n\t\t\torderByMedian: s.orderByMedian,\n\t\t\tfilter: this.state.termfilter.filter\n\t\t}\n\n\t\tif (this.opts.mode == 'minimal') {\n\t\t\targ.tw = term\n\t\t\t// assume a single term for minimal plot\n\t\t\tif (term2 || term0) throw 'only a single term allowed for minimal plot'\n\t\t\tif (term.q.mode == 'spline') {\n\t\t\t\t/** FIXME bad design; should not modify setting or even plot state in runtime, \n\t\t\t\tinstead supply this in constructor arg and generalize it beyond spline\n\t\t\t\t// term may be cubic spline from regression analysis\n\t\t\t\t// render knot values as vertical lines on the plot\n\t\t\t\t*/\n\t\t\t\ts.lines = term.q.knots.map(x => Number(x.value))\n\t\t\t} else {\n\t\t\t\ts.lines = []\n\t\t\t}\n\t\t\tif (term.q.scale) {\n\t\t\t\t// term may be scaled from regression analysis\n\t\t\t\t// scale the data on the server-side\n\t\t\t\targ.scale = term.q.scale\n\t\t\t}\n\t\t} else if (isNumericTerm(term.term) && term.q.mode === 'continuous') {\n\t\t\targ.tw = term\n\t\t\tif (term2) arg.overlayTw = term2\n\t\t} else if (isNumericTerm(term2?.term) && term2.q.mode === 'continuous') {\n\t\t\targ.tw = term2\n\t\t\targ.overlayTw = term\n\t\t} else {\n\t\t\tthrow 'both term1 and term2 are not numeric/continuous'\n\t\t}\n\n\t\tif (term0) arg.divideTw = term0\n\t\treturn arg\n\t}\n}\n\nexport const violinInit = getCompInit(ViolinPlot)\nexport const componentInit = violinInit\n\nexport function getDefaultViolinSettings(app, overrides = {}) {\n\tconst defaults = {\n\t\torientation: 'horizontal',\n\t\trowlabelw: 250,\n\t\tbrushRange: null, //object with start and end if there is a brush selection\n\t\tsvgw: 500, // span length of a plot/svg, not including margin\n\t\tdatasymbol: 'rug',\n\t\tradius: 10,\n\t\taxisHeight: 60,\n\t\trightMargin: 50,\n\t\tlines: [],\n\t\tunit: 'abs', // abs: absolute scale, log: log scale\n\t\trowSpace: 10,\n\t\tmedianLength: 7,\n\t\tmedianColor: '#FF0000',\n\t\tmedianThickness: 3,\n\t\tticks: 15,\n\t\tdefaultColor: plotColor,\n\t\tmethod: 0,\n\t\torderByMedian: false,\n\t\tshowStats: true,\n\t\tshowAssociationTests: true\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'violin getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tthrow `${e} [violin getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\t// common: {\n\t\t\t// \tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t// \tuse_percentage: false,\n\t\t\t// \tbarheight: 300, // maximum bar length\n\t\t\t// \tbarwidth: 20, // bar thickness\n\t\t\t// \tbarspace: 2 // space between two bars\n\t\t\t// },\n\t\t\tviolin: getDefaultViolinSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
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+  "names": []
+}

package/dist/{chunk-FXA25J4U.js → chunk-MO2UD3ZX.js}

@@ -9,13 +9,13 @@ import {
   rgb2hex,
   table2col,
   termsettingInit
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
 import {
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   NUMERIC_DICTIONARY_TERM,
   TermTypes,
@@ -242,7 +242,7 @@ function setInteractivity(self) {
         const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp-ssgp-menu-btn").text(k).on("click", async (event3) => {
           const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
           sandbox.header.text(sample.sample_id);
-          await (await import("./plot.ssgq-LIEYVBR6.js")).plotSingleSampleGenomeQuantification(
+          await (await import("./plot.ssgq-K5WT5SRR.js")).plotSingleSampleGenomeQuantification(
             self.state.termdbConfig,
             self.state.vocab.dslabel,
             k,
@@ -260,7 +260,7 @@ function setInteractivity(self) {
       const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "oncoMatrix_termLabel_disco_button").text("Disco plot").on("click", async (event3) => {
         const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
         sandbox.header.text(sample.sample_id);
-        (await import("./plot.disco-BOW777AK.js")).default(
+        (await import("./plot.disco-DY6FSDYY.js")).default(
           self.state.termdbConfig,
           self.state.vocab.dslabel,
           sample,
@@ -286,7 +286,7 @@ function setInteractivity(self) {
         menuDiv.on("click", async (_) => {
           const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
           sandbox.header.text(sample.sample_id);
-          (await import("./plot.dzi-S7Y6FJGL.js")).default(
+          (await import("./plot.dzi-IY3ZDIBG.js")).default(
             self.state.vocab.dslabel,
             sandbox.body,
             self.app.opts.genome,
@@ -947,7 +947,7 @@ function setTermActions(self) {
         usecase.detail = "term";
       }
     }
-    const termdb = await import("./app-WTWHDUA6.js");
+    const termdb = await import("./app-2RFP3X67.js");
     holder.selectAll("*").remove();
     termdb.appInit({
       holder: holder.append("div"),
@@ -1262,7 +1262,7 @@ function setSampleGroupActions(self) {
     label2.append("input").attr("type", "radio").attr("name", radioName).attr("value", "term0");
     label2.append("span").html(" divide");
     self.dom.menubody.append("div").style("padding-bottom", "10px").html(`the selected survival variable below:`);
-    const termdb = await import("./app-WTWHDUA6.js");
+    const termdb = await import("./app-2RFP3X67.js");
     termdb.appInit({
       holder: self.dom.menubody.append("div"),
       vocabApi: self.app.vocabApi,
@@ -2669,4 +2669,4 @@ export {
   getConfigForShowAll,
   showAll
 };
-//# sourceMappingURL=chunk-FXA25J4U.js.map
+//# sourceMappingURL=chunk-MO2UD3ZX.js.map

package/dist/{chunk-WHJTQR5P.js → chunk-MRCJES3F.js}

@@ -1,6 +1,6 @@
 import {
   searchSampleInput
-} from "./chunk-EJSNAJBJ.js";
+} from "./chunk-GRNOZADJ.js";
 import {
   ScatterModel,
   ScatterView,
@@ -8,7 +8,7 @@ import {
   ScatterViewModel2DLarge,
   getContourImage,
   getThreeCircle
-} from "./chunk-HJGGXQZ5.js";
+} from "./chunk-NCANCAZ3.js";
 import {
   AxesHelper,
   BufferGeometry,
@@ -31,7 +31,7 @@ import {
 } from "./chunk-72PLI3GC.js";
 import {
   getId
-} from "./chunk-VCZQJQIS.js";
+} from "./chunk-QWMTKXKY.js";
 import {
   DownloadMenu,
   PlotBase,
@@ -45,7 +45,7 @@ import {
   newSandboxDiv,
   rebaseGroupFilter,
   select2Terms
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -103,7 +103,7 @@ var ScatterInteractivity = class {
     for (const k in this.scatter.state.termdbConfig.queries.singleSampleGenomeQuantification) {
       const sandbox = newSandboxDiv(this.scatter.opts.plotDiv);
       sandbox.header.text(sample.sample_id);
-      const ssgqImport = await import("./plot.ssgq-LIEYVBR6.js");
+      const ssgqImport = await import("./plot.ssgq-K5WT5SRR.js");
       await ssgqImport.plotSingleSampleGenomeQuantification(
         this.scatter.state.termdbConfig,
         this.scatter.state.vocab.dslabel,
@@ -121,7 +121,7 @@ var ScatterInteractivity = class {
     sample.sample_id = sample.sample;
     const sandbox = newSandboxDiv(this.scatter.opts.plotDiv || select_default(this.scatter.opts.holder.node().parentNode));
     sandbox.header.text(sample.sample_id);
-    const discoPlotImport = await import("./plot.disco-BOW777AK.js");
+    const discoPlotImport = await import("./plot.disco-DY6FSDYY.js");
     discoPlotImport.default(
       this.scatter.state.termdbConfig,
       this.scatter.state.vocab.dslabel,
@@ -149,7 +149,7 @@ var ScatterInteractivity = class {
         }
       ]
     };
-    const _ = await import("./block.init-4WT3S577.js");
+    const _ = await import("./block.init-Q7QL52CR.js");
     await _.default(arg);
   }
   async searchSample(e) {
@@ -797,4 +797,4 @@ export {
   getDefaultScatterSettings,
   openScatterPlot
 };
-//# sourceMappingURL=chunk-WHJTQR5P.js.map
+//# sourceMappingURL=chunk-MRCJES3F.js.map

package/dist/{chunk-HJGGXQZ5.js → chunk-NCANCAZ3.js}

@@ -23,7 +23,7 @@ import {
 } from "./chunk-72PLI3GC.js";
 import {
   getId
-} from "./chunk-VCZQJQIS.js";
+} from "./chunk-QWMTKXKY.js";
 import {
   ColorScale,
   Tabs,
@@ -42,13 +42,13 @@ import {
   shapeSelector,
   shapesArray,
   table2col
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
 import {
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   TermTypes,
   getDateFromNumber,
@@ -1525,7 +1525,11 @@ var ScatterView = class {
         title: "Term to to divide by categories or to use as Z coordinate",
         label: "Z / Divide by",
         vocabApi: this.scatter.app.vocabApi,
-        numericEditMenuVersion: ["discrete", "continuous"],
+        // do not allow 'continuous' mode for now, even if it can be rendered along z-axis,
+        // since clicking to barchart/violin/boxplot tab from the scatter tab does not
+        // automatically convert the divide-by term to discrete; a continuous mode in those
+        // other charts leads to nonsensical chart per unique float/integer value
+        numericEditMenuVersion: ["discrete"],
         processInput: (tw) => {
           if (!isPremade && isNumericTerm(tw?.term)) tw.q = { mode: "continuous" };
         }
@@ -3260,7 +3264,7 @@ var singleCellPlot = class {
         ]
       }
     };
-    const plotImport = await import("./plot.app-PZAOK7XL.js");
+    const plotImport = await import("./plot.app-QJM2LU3Q.js");
     const plotAppApi = await plotImport.appInit(opts);
   }
   async renderGSEA(holder) {
@@ -3287,7 +3291,7 @@ var singleCellPlot = class {
         plots: [config]
       }
     };
-    const plotImport = await import("./plot.app-PZAOK7XL.js");
+    const plotImport = await import("./plot.app-QJM2LU3Q.js");
     const plotAppApi = await plotImport.appInit(opts);
   }
   async renderDETable() {
@@ -4170,4 +4174,4 @@ export {
   getPlotConfig,
   getDefaultSingleCellSettings
 };
-//# sourceMappingURL=chunk-HJGGXQZ5.js.map
+//# sourceMappingURL=chunk-NCANCAZ3.js.map