@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-36DYWBU7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.layout.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { schemeCategory10, interpolateReds, interpolateBlues } from 'd3-scale-chromatic'\nimport { axisLeft, axisTop, axisRight, axisBottom } from 'd3-axis'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv } from '#shared/common.js'\nimport { colorDelta, getInterpolatedDomainRange, removeInterpolatedOutliers, removeOutliers } from '#dom'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\nconst MINCOLWSPACED = 7\n\nexport function setAutoDimensions(xOffset) {\n\tconst m = this.state.config.settings.matrix\n\tif (!this.autoDimensions) this.autoDimensions = new Set()\n\n\t// NOTE: there may be a hardcoded m.colw = 0 in matrix.config to force auto-sizing\n\tif (!m.colw) this.autoDimensions.add('colw')\n\telse this.autoDimensions.delete('colw')\n\tif (!m.rowh) this.autoDimensions.add('rowh')\n\telse this.autoDimensions.delete('rowh')\n\n\tconst s = this.settings.matrix\n\tthis.computedSettings = {\n\t\tuseCanvas: this.sampleOrder.length > m.svgCanvasSwitch\n\t}\n\n\tif (s.availContentWidth) {\n\t\tthis.availContentWidth = s.availContentWidth\n\t} else {\n\t\tlet boundingWidth = this.dom.contentNode.getBoundingClientRect().width\n\t\tif (boundingWidth < 600) {\n\t\t\t// rely on div scroll to view a not-overly-narrow matrix\n\t\t\tboundingWidth = window.document.body.clientWidth\n\t\t}\n\n\t\t// 65 is an mannually calibrated padding\n\t\tconst maxGrpLabelWidth = this.getMaxGrpLabelWidth()\n\t\tconst padding = Math.max(65, maxGrpLabelWidth)\n\n\t\t// should be estimated based on label-fontsize and longest label\n\t\t// const labelOffset = !s.transpose\n\t\t// \t? s.termLabelOffset + s.termGrpLabelOffset\n\t\t// \t: s.sampleLabelOffset + s.sampleGrpLabelOffset\n\t\tconst hcw = this.state.config.settings.hierCluster?.xDendrogramHeight || 0\n\t\tthis.availContentWidth = boundingWidth - padding - s.margin.right - xOffset - hcw // - 0.5 * labelOffset\n\t}\n\n\tlet colwSpaced, colwNoSpace\n\tif (this.autoDimensions.has('colw')) {\n\t\tconst totalColgspace = s.colgspace * Math.max(0, this.visibleSampleGrps.size - 1)\n\t\tconst tentativeGaps = this.sampleOrder.length * s.colspace + totalColgspace\n\t\tconst spacedColw = (this.availContentWidth - tentativeGaps) / this.sampleOrder.length\n\t\tconst constrainedMINCOLWSPACED = Math.max(s.colwMin, Math.min(MINCOLWSPACED, s.colwMax))\n\t\t// colwSpaced is the colw if the colspace is shown between columns, but note that\n\t\t// its value does not include the colspace. It also requires MINCOLWSPACED column width\n\t\t// for the colspace to not be too visually overwhelming.\n\t\tcolwSpaced = Math.max(constrainedMINCOLWSPACED, Math.min(spacedColw, s.colwMax))\n\t\t// noSpacedColw is the colw if the colspace is not shown between columns, without taking into account colwMin and colwMax\n\t\tconst noSpacedColw = (this.availContentWidth - totalColgspace) / this.sampleOrder.length\n\t\t// colwNoSpace is the colw if the colspace is not shown between columns, after taking into account colwMin and colwMax\n\t\tcolwNoSpace = Math.max(s.colwMin, Math.min(noSpacedColw, s.colwMax))\n\n\t\t// if the computed colwSpaced for (availContentWidth - gaps) / (numer of samples) is less than MINCOLWSPACED,\n\t\t// then rendered gaps between columns will be visually overwhelming, use colwNoSpace in that case\n\t\tthis.computedSettings.colw = colwSpaced <= MINCOLWSPACED ? colwNoSpace : colwSpaced\n\n\t\t// IMPORTANT: compute zoomMin and zoomMax here before computing settings.colw downstream\n\t\t// in setLayout(), to avoid feedback loop\n\t\tthis.computedSettings.zoomMin = s.colwMin / this.computedSettings.colw\n\t\tthis.computedSettings.zoomMax = s.colwMax / this.computedSettings.colw\n\t} else {\n\t\tcolwSpaced = m.colw\n\t\tcolNoSpace = m.colw\n\t\t// NOTE: There may be a hardcoded m.colw = 0 in matrix.config to force auto-sizing,\n\t\t// handling this condition for future support.\n\t\tthis.computedSettings.colw = m.colw\n\t\tthis.computedSettings.zoomMin = s.colwMin / m.colw\n\t\tthis.computedSettings.zoomMax = s.colwMax / m.colw\n\t}\n\n\tconst { colw } = this.computedSettings\n\t// When cells have very small width, do not show colspace. If colwSpaced == colwNoSpace,\n\t// that means max\n\t// IMPORTANT: compute zoomMin and zoomMax before using s.zoomLevel for any computed settings\n\tthis.computedSettings.colspace =\n\t\t(colw === colwNoSpace && colwSpaced < colwNoSpace) || colw * s.zoomLevel < MINCOLWSPACED ? 0 : s.colspace\n\n\tconst hch = this.state.config.settings.hierCluster?.yDendrogramHeight || 0\n\tconst availHeight = s.availContentHeight || screen.availHeight - hch\n\tthis.computedSettings.clusterRowh = Math.min(\n\t\ts.rowhMax,\n\t\tMath.max(s.rowhMin, Math.floor(availHeight / this.numClusterTerms))\n\t)\n\tcopyMerge(this.settings.matrix, this.computedSettings)\n}\n\n// calculate the max group label width on the plot\nexport function getMaxGrpLabelWidth() {\n\tconst s = this.settings.matrix\n\n\t// attach each group label on tmp g (later removed) to calculate the max actual width of the group label on plot\n\tconst g = this.dom.svg.append('g').attr('opacity', 0.01)\n\tlet maxWidth = 0\n\tfor (const grp of this.termGroups) {\n\t\tconst grpLabel = !grp.name\n\t\t\t? ''\n\t\t\t: grp.name.length <= s.termGrpLabelMaxChars\n\t\t\t? grp.name\n\t\t\t: grp.name.slice(0, s.termGrpLabelMaxChars) + '\u2026'\n\t\tconst text = g.append('text').text(grpLabel).attr('font-size', 12)\n\t\tconst box = text.node().getBBox()\n\t\tif (maxWidth < box.width) maxWidth = box.width\n\t}\n\tg.remove()\n\treturn maxWidth\n}\n\nexport function setLabelsAndScales() {\n\tconst s = this.settings.matrix\n\tthis.cnvValues = []\n\t// ht: standard cell dimension for term row or column\n\tconst ht = s.transpose ? s.colw : s.rowh\n\tconst grpTotals = {}\n\tconst processedLabels = { sampleGrpByName: {}, termGrpByName: {} }\n\tlet totalHtAdjustments = 0\n\n\tfor (const t of this.termOrder) {\n\t\tconst countedSamples = new Set()\n\t\tt.counts = { samples: 0, hits: 0 }\n\t\tconst renderedContinuousVs = []\n\t\t// Track if any sample in this term has mixed positive/negative values\n\t\tlet hasMixedValues = false\n\n\t\t// Initialize min/max for termCollection\n\t\tif (t.tw.term.type == 'termCollection') {\n\t\t\tt.counts.minval = 0\n\t\t\tt.counts.maxval = 0\n\t\t}\n\n\t\t// store counts for each subGroup in subGroupCounts\n\t\tt.counts.subGroupCounts = {}\n\t\tfor (const group of this.sampleGroups) {\n\t\t\tt.counts.subGroupCounts[group.name] = {\n\t\t\t\tsamplesTotal: 0, // number of counted (not Blank or WT) samples\n\t\t\t\tclasses: {} // number of each class\n\t\t\t}\n\t\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\t\t// for a geneVariant term, the number of samples not tested\n\t\t\t\tt.counts.subGroupCounts[group.name].samplesNotTested = 0 //number of samples not tested\n\t\t\t}\n\t\t}\n\t\tif (!processedLabels.termGrpByName[t.grp.name || '']) {\n\t\t\tconst name = t.grp.name || ''\n\t\t\tt.grp.label = name.length <= s.termGrpLabelMaxChars ? name : name.slice(0, s.termGrpLabelMaxChars) + '\u2026'\n\t\t\tprocessedLabels.termGrpByName[name] = t.grp.label\n\t\t}\n\t\tfor (const sample of this.sampleOrder) {\n\t\t\tif (countedSamples.has(sample.row.sample)) continue\n\t\t\tconst name = sample.grp.name || ''\n\t\t\tif (!(name in processedLabels.sampleGrpByName)) {\n\t\t\t\tsample.grp.label =\n\t\t\t\t\tname.length <= s.sampleGrpLabelMaxChars ? name : name.slice(0, s.sampleGrpLabelMaxChars) + '\u2026'\n\t\t\t\tif (this.config.divideBy) sample.grp.label += ` (${sample.grp.lst.length})`\n\t\t\t\tprocessedLabels.sampleGrpByName[name] = sample.grp.label\n\t\t\t}\n\t\t\tconst sampleName = sample.row._ref_.label || ''\n\t\t\tsample.label =\n\t\t\t\tsampleName.length <= s.collabelmaxchars ? sampleName : sampleName.slice(0, s.collabelmaxchars) + '\u2026'\n\n\t\t\tconst anno = sample.row[t.tw.$id]\n\t\t\tif (!anno) continue\n\n\t\t\t// Check if this annotation has mixed positive/negative values (for termCollection)\n\t\t\tif (t.tw.term.type == 'termCollection' && anno.hasMixedValues) {\n\t\t\t\thasMixedValues = true\n\t\t\t}\n\n\t\t\t// Track min/max percentage values for termCollection\n\t\t\tif (t.tw.term.type == 'termCollection' && anno.values) {\n\t\t\t\tfor (const val of anno.values) {\n\t\t\t\t\tconst pct = val.value\n\t\t\t\t\tif (pct > 0) {\n\t\t\t\t\t\t// For positive values, track the cumulative sum (pre_val_sum + pct)\n\t\t\t\t\t\tconst cumSum = val.pre_val_sum + pct\n\t\t\t\t\t\tif (!('maxval' in t.counts) || t.counts.maxval < cumSum) {\n\t\t\t\t\t\t\tt.counts.maxval = cumSum\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (pct < 0) {\n\t\t\t\t\t\t// For negative values, track the cumulative sum (pre_val_sum + pct, which is negative)\n\t\t\t\t\t\tconst cumSum = val.pre_val_sum + pct\n\t\t\t\t\t\tif (!('minval' in t.counts) || t.counts.minval > cumSum) {\n\t\t\t\t\t\t\tt.counts.minval = cumSum\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// This is the second call to classifyValues(), to determine case/hit counts for row labels\n\t\t\tconst { filteredValues, countedValues, renderedValues } = this.classifyValues(\n\t\t\t\tanno,\n\t\t\t\tt.tw,\n\t\t\t\tt.grp,\n\t\t\t\tthis.settings.matrix,\n\t\t\t\tsample.row\n\t\t\t)\n\t\t\tanno.filteredValues = filteredValues\n\t\t\tanno.countedValues = countedValues\n\t\t\tanno.renderedValues = renderedValues\n\t\t\tif (anno.countedValues?.length) {\n\t\t\t\tt.counts.samples += 1\n\t\t\t\tt.counts.hits += anno.countedValues.length\n\t\t\t\tif (t.tw.q?.mode == 'continuous') {\n\t\t\t\t\tconst v = anno.value\n\t\t\t\t\tif (!t.tw.term.values?.[v]?.uncomputable) {\n\t\t\t\t\t\tif (!('minval' in t.counts) || t.counts.minval > v) t.counts.minval = v\n\t\t\t\t\t\tif (!('maxval' in t.counts) || t.counts.maxval < v) t.counts.maxval = v\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (t.tw.term.type == 'geneVariant' && anno.values) {\n\t\t\t\t\tfor (const val of anno.values) {\n\t\t\t\t\t\tif (val.dt == dtcnv && 'value' in val && !s.ignoreCnvValues) {\n\t\t\t\t\t\t\tconst v = val.value\n\t\t\t\t\t\t\tthis.cnvValues.push(v)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (t.tw.q?.mode == 'continuous' && renderedValues?.length && t.grp.type != 'hierCluster') {\n\t\t\t\t// store the rendered continuous values into renderedContinuousVs to be used later\n\t\t\t\t// do not do it for terms in hierCluster group\n\t\t\t\trenderedContinuousVs.push(\n\t\t\t\t\tt.tw.term.valueConversion\n\t\t\t\t\t\t? t.tw.term.valueConversion.scaleFactor * (renderedValues[0].value || renderedValues[0])\n\t\t\t\t\t\t: renderedValues[0].value || renderedValues[0]\n\t\t\t\t)\n\t\t\t}\n\n\t\t\tconst subGroup = t.counts.subGroupCounts?.[sample.grp.name]\n\n\t\t\tconst countedValuesNoSkip = anno.filteredValues.filter(v => {\n\t\t\t\t// doesn't consider geneVariantCountSamplesSkipMclass as countedValues does\n\t\t\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\t\t\t// do not count wildtype and not tested as hits\n\t\t\t\t\tif (v.class == 'WT' || v.class == 'Blank') return false\n\t\t\t\t}\n\t\t\t\treturn true\n\t\t\t})\n\n\t\t\tif (countedValuesNoSkip.length) {\n\t\t\t\t//count the samples and classes in each subGroup\n\t\t\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\t\t\tlet sampleCounted = false\n\t\t\t\t\tfor (const countedValue of countedValuesNoSkip) {\n\t\t\t\t\t\tif (s.geneVariantCountSamplesSkipMclass.includes(countedValue.class)) {\n\t\t\t\t\t\t\tif (!subGroup.notTestedClasses) subGroup.notTestedClasses = {}\n\t\t\t\t\t\t\tif (!(countedValue.class in subGroup.notTestedClasses)) subGroup.notTestedClasses[countedValue.class] = 1\n\t\t\t\t\t\t\telse subGroup.notTestedClasses[countedValue.class] += 1\n\t\t\t\t\t\t} else if (!(countedValue.class in subGroup.classes)) {\n\t\t\t\t\t\t\tif (!sampleCounted) {\n\t\t\t\t\t\t\t\tsubGroup.samplesTotal += 1\n\t\t\t\t\t\t\t\tsampleCounted = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tsubGroup.classes[countedValue.class] = 1\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (!sampleCounted) {\n\t\t\t\t\t\t\t\tsubGroup.samplesTotal += 1\n\t\t\t\t\t\t\t\tsampleCounted = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tsubGroup.classes[countedValue.class] += 1\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tsubGroup.samplesTotal += 1\n\t\t\t\t\tfor (const countedValue of countedValuesNoSkip) {\n\t\t\t\t\t\tif (!(countedValue in subGroup.classes)) subGroup.classes[countedValue] = 1\n\t\t\t\t\t\telse subGroup.classes[countedValue] += 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (anno.filteredValues?.length && t.tw.term.type == 'geneVariant') {\n\t\t\t\t//count the samples that are not tested in each subGroup\n\t\t\t\tconst notTested = anno.filteredValues.every(v => v.class == 'Blank')\n\t\t\t\tif (notTested) {\n\t\t\t\t\t// sample not tested for all assays\n\t\t\t\t\tsubGroup.samplesNotTested += 1\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (t.tw.label) {\n\t\t\tt.label = t.tw.label\n\t\t} else if (t.grp.type == 'hierCluster') {\n\t\t\tt.label = t.tw.term.gene || t.tw.term.name\n\t\t} else {\n\t\t\tt.label = t.tw.term.name\n\t\t}\n\t\tif (t.label.length > s.rowlabelmaxchars) t.label = t.label.slice(0, s.rowlabelmaxchars - 1) + '\u2026'\n\t\tconst termGroupName = this.config?.settings.hierCluster?.termGroupName\n\t\tif (s.samplecount4gene && t.tw.term.type.startsWith('gene') && (!termGroupName || t.grp.name !== termGroupName)) {\n\t\t\tconst count =\n\t\t\t\ts.samplecount4gene === 'abs'\n\t\t\t\t\t? t.counts.samples\n\t\t\t\t\t: ((100 * t.counts.samples) / this.sampleOrder.length).toFixed(1) + '%'\n\t\t\tt.label = `${t.label} (${count})`\n\t\t}\n\n\t\tconst twSpecificSettings = this.config.settings.matrix.twSpecificSettings\n\t\tif (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {}\n\t\tconst twSettings = twSpecificSettings[t.tw.$id]\n\n\t\tif (t.grp.type !== 'hierCluster' && t.tw.q?.mode == 'continuous') {\n\t\t\tconst vc = t.tw.term.valueConversion\n\t\t\tif (vc) {\n\t\t\t\t// convert values\n\t\t\t\tt.counts.minval *= vc.scaleFactor\n\t\t\t\tt.counts.maxval *= vc.scaleFactor\n\t\t\t}\n\n\t\t\t/*\n\t\t\t\tcompute mean and std on the client side using the renderedValues, instead of asking the server to \n\t\t\t\ttransform the values when the data source does not actually change. That means re-reading \n\t\t\t\tdb/files/external API for the same data on the server, it would impact the server less \n\t\t\t\t(by allowing caching and offloading computation) if the value transformation is done on \n\t\t\t\tthe client. Also, in case some of the data/rendered filters are done on the client-side plot, \n\t\t\t\tthen the server may not know which data are actually rendered, meaning the mean and stdev \n\t\t\t\tmay not be computable on the server side.\n\t\t\t*/\n\t\t\tif (renderedContinuousVs.length && t.tw.q.convert2ZScore) {\n\t\t\t\tconst mean = renderedContinuousVs.reduce((acc, val) => acc + val, 0) / renderedContinuousVs.length\n\t\t\t\tconst std = Math.sqrt(\n\t\t\t\t\trenderedContinuousVs.reduce((acc, val) => acc + Math.pow(val - mean, 2), 0) / renderedContinuousVs.length\n\t\t\t\t)\n\t\t\t\tt.mean = mean\n\t\t\t\tt.std = std\n\t\t\t\tt.counts.minval = (t.counts.minval - mean) / std\n\t\t\t\tt.counts.maxval = (t.counts.maxval - mean) / std\n\t\t\t}\n\n\t\t\tif (!twSettings.contBarH) twSettings.contBarH = t.tw.term.type == 'termCollection' ? 150 : s.barh\n\t\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\t\t\tconst barh = twSettings.contBarH\n\t\t\t// For termCollection, min/max values are already calculated from the percentage values\n\t\t\t// No need to force specific ranges - use dynamic range based on actual data\n\t\t\tif (t.tw.term.type == 'termCollection') {\n\t\t\t\t// Ensure minval and maxval are set (default to 0 if no values)\n\t\t\t\tif (!('minval' in t.counts)) t.counts.minval = 0\n\t\t\t\tif (!('maxval' in t.counts)) t.counts.maxval = 0\n\t\t\t}\n\n\t\t\tconst absMin = Math.abs(t.counts.minval)\n\t\t\tconst rangeSpansZero = t.counts.minval < 0 && t.counts.maxval > 0\n\t\t\tconst ratio = t.counts.minval >= 0 ? 1 : t.counts.maxval / (absMin + t.counts.maxval)\n\t\t\tt.counts.posMaxHt = ratio * barh\n\t\t\tconst tickValues = [t.counts.maxval, t.counts.minval]\n\t\t\tt.scales = {\n\t\t\t\ttickValues,\n\t\t\t\tfull: scaleLinear().domain(tickValues).range([1, barh])\n\t\t\t}\n\t\t\tif (t.counts.maxval >= 0) {\n\t\t\t\tconst domainMin = rangeSpansZero ? 0 : t.counts.minval\n\t\t\t\tt.scales.pos = scaleLinear().domain([domainMin, t.counts.maxval]).range([1, t.counts.posMaxHt])\n\t\t\t}\n\t\t\tif (t.counts.minval < 0) {\n\t\t\t\tconst domainMax = rangeSpansZero ? 0 : t.counts.maxval\n\t\t\t\tt.scales.neg = scaleLinear()\n\t\t\t\t\t.domain([domainMax, t.counts.minval])\n\t\t\t\t\t.range([1, barh - t.counts.posMaxHt])\n\t\t\t}\n\t\t}\n\n\t\tt.totalHtAdjustments = totalHtAdjustments\n\t\tt.rowHt =\n\t\t\tt.grp.type == 'hierCluster'\n\t\t\t\t? s.clusterRowh\n\t\t\t\t: twSettings.contBarH && t.tw.q?.mode == 'continuous'\n\t\t\t\t? twSettings.contBarH + 2 * twSettings.contBarGap\n\t\t\t\t: ht\n\t\t// adjustment is the difference in actual computed row height - \"standard\" row\n\t\t// need to subtract s.rowspace for hierCluster row to remove gaps between heatmap rows\n\t\tconst adjustment = t.rowHt - ht - (t.grp.type == 'hierCluster' ? s.rowspace : 0)\n\t\ttotalHtAdjustments += adjustment\n\n\t\t// adjustment when last row is in continous mode\n\t\tt.cumulativeAdjustment = totalHtAdjustments\n\n\t\tif (!(t.visibleGrpIndex in grpTotals)) grpTotals[t.visibleGrpIndex] = { htAdjustment: 0 }\n\t\tgrpTotals[t.visibleGrpIndex].htAdjustment += adjustment\n\t\tt.grpTotals = grpTotals[t.visibleGrpIndex]\n\t}\n\n\tlet cnvLegendDomainRange // if cnv data is present, compute once and reuse across geneVariant tw's\n\n\tif (this.cnvValues.length) {\n\t\tif (s.cnvValues.cutoffMode == 'fixed') {\n\t\t\tthis.cnvValues = this.cnvValues.filter(v => v >= s.cnvValues.min && v <= s.cnvValues.max).sort((a, b) => a - b)\n\t\t\t//Need to include the input value for the user\n\t\t\tif (this.cnvValues[0] != s.cnvValues.min) this.cnvValues.unshift(s.cnvValues.min)\n\t\t\tif (this.cnvValues[this.cnvValues.length - 1] != s.cnvValues.max) this.cnvValues.push(s.cnvValues.max)\n\t\t} else if (s.cnvValues.cutoffMode == 'percentile' || s.cnvValues.cutoffMode == 'auto') {\n\t\t\t/** Users enter the percentile as whole number.\n\t\t\t * Convert to a fraction for removeOutliers.*/\n\t\t\tlet maxPercentile = s.cnvValues.cutoffMode == 'auto' ? s.cnvValues.defaultPercentile : s.cnvValues.percentile\n\t\t\tmaxPercentile = maxPercentile / 100\n\t\t\tconst minPercentile = roundValueAuto(1 - maxPercentile)\n\t\t\tthis.cnvValues = removeOutliers(this.cnvValues, { minPercentile, maxPercentile, baseValue: 0 })\n\t\t} else throw new Error(`Invalid cnvValues cutoffMode: ${s.cnvValues.cutoffMode}`)\n\t\tconst minLoss = this.cnvValues[0] <= 0 ? this.cnvValues[0] : undefined\n\t\tconst maxGain =\n\t\t\tthis.cnvValues[this.cnvValues.length - 1] >= 0 ? this.cnvValues[this.cnvValues.length - 1] : undefined\n\t\tlet maxLoss, minGain, absMax\n\t\tfor (const n of this.cnvValues) {\n\t\t\tif (n < 0) maxLoss = n\n\t\t\tif (!minGain && n > 0) {\n\t\t\t\tminGain = n\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\t// need to assign scales to terms after the loop above so each term has the global maxLoss, maxGain, minLoss, minGain\n\t\tfor (const t of this.termOrder) {\n\t\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\t\tif (!cnvLegendDomainRange) {\n\t\t\t\t\t// compute these interpolated domain/range only once,\n\t\t\t\t\t// and then share with other t objects\n\t\t\t\t\tconst loss0color = interpolateBlues(0)\n\t\t\t\t\tconst gain0color = interpolateReds(0)\n\t\t\t\t\tconst colorDiff = colorDelta(loss0color, gain0color)\n\t\t\t\t\tif (minLoss !== undefined && maxGain !== undefined && colorDiff > 25)\n\t\t\t\t\t\tconsole.warn(\n\t\t\t\t\t\t\t`CNV loss and gain do not have the same middle color for value=0` +\n\t\t\t\t\t\t\t\t`'${loss0color}' vs '${gain0color}', color difference=${colorDiff}`\n\t\t\t\t\t\t)\n\n\t\t\t\t\t// These precomputed CNV domains and ranges are to be passed to\n\t\t\t\t\t// ColorScale legend renderer in matrix.legend.js. By computing\n\t\t\t\t\t// these values here, the legend will match the scale\n\t\t\t\t\t// min/max values and rendered-value colors in matrix cells.\n\t\t\t\t\tabsMax =\n\t\t\t\t\t\tminLoss !== undefined && maxGain !== undefined\n\t\t\t\t\t\t\t? Math.max(Math.abs(minLoss), maxGain)\n\t\t\t\t\t\t\t: minLoss !== undefined\n\t\t\t\t\t\t\t? Math.abs(minLoss)\n\t\t\t\t\t\t\t: maxGain\n\t\t\t\t\tcnvLegendDomainRange = getInterpolatedDomainRange({\n\t\t\t\t\t\tabsMin: 0,\n\t\t\t\t\t\tabsMax,\n\t\t\t\t\t\ttotalNumSteps: 10,\n\t\t\t\t\t\tnegInterpolator: minLoss !== undefined && interpolateBlues,\n\t\t\t\t\t\tposInterpolator: maxGain !== undefined && interpolateReds,\n\t\t\t\t\t\t// force this middleColor to white, knowing that interpolateBlues and interpolateReds,\n\t\t\t\t\t\t// as hardcoded above and below, share similar white colors for their minimum abs values\n\t\t\t\t\t\tmiddleColor: 'white'\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\t// const min = cnvLegendDomainRange.domain[0]\n\t\t\t\t// const max = cnvLegendDomainRange.domain[cnvLegendDomainRange.domain.length - 1]\n\t\t\t\t// const domainRange = Math.abs(max - min)\n\t\t\t\t// if (((min === 0 || max === 0) && domainRange > 1) || domainRange > 5)\n\t\t\t\t// cnvLegendDomainRange = removeInterpolatedOutliers(cnvLegendDomainRange)\n\n\t\t\t\tt.scales = {\n\t\t\t\t\tloss: interpolateBlues,\n\t\t\t\t\tgain: interpolateReds,\n\t\t\t\t\tmaxLoss,\n\t\t\t\t\tmaxGain,\n\t\t\t\t\tminLoss,\n\t\t\t\t\tminGain,\n\t\t\t\t\tabsMax,\n\t\t\t\t\tlegend: cnvLegendDomainRange\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function setLayout() {\n\tconst s = this.settings.matrix\n\tconst [col, row] = !s.transpose ? ['sample', 'term'] : ['term', 'sample']\n\tconst [_t_, _b_] = s.collabelpos == 'top' ? ['', 'Grp'] : ['Grp', '']\n\tconst [_l_, _r_] = s.rowlabelpos == 'left' ? ['', 'Grp'] : ['Grp', '']\n\tconst top = col + _t_\n\tconst btm = col + _b_\n\tconst left = row + _l_\n\tconst right = row + _r_\n\n\t// TODO: should not need aliases, rename class properties to simplify\n\tthis.samples = this.sampleOrder\n\tthis.sampleGrps = this.sampleOrder.filter(s => s.index === 0)\n\tthis.terms = this.termOrder\n\tthis.termGrps = this.termOrder.filter(t => t.index === 0)\n\n\tconst layout = {}\n\tconst sides = { top, btm, left, right }\n\tfor (const direction in sides) {\n\t\tconst d = sides[direction]\n\t\tconst Direction = direction[0].toUpperCase() + direction.slice(1)\n\t\tlayout[direction] = {\n\t\t\tprefix: d,\n\t\t\tdata: this[`${d}s`],\n\t\t\toffset: s[`${d}LabelOffset`],\n\t\t\tbox: this.dom[`${d}LabelG`],\n\t\t\tkey: this[`${d}Key`],\n\t\t\tlabel: this[`${d}Label`],\n\t\t\trender: this[`render${Direction}Label`],\n\t\t\tisGroup: sides[direction].includes('Grp')\n\t\t}\n\t}\n\n\tconst yOffset = layout.top.offset + s.margin.top + s.scrollHeight\n\tconst xOffset = layout.left.offset + s.margin.left\n\n\tthis.setAutoDimensions(xOffset)\n\tthis.setLabelsAndScales()\n\n\t// When the cell is very small, colspace is 0. Once zoomed in, colspace will be shown, so need to consider it when zooming in\n\t// At this point, computed matrix settings has been merged to settings.matrix by setAutoDimensions.\n\tconst colw = Math.max(s.colwMin, Math.min(s.colwMax, s.colw * s.zoomLevel))\n\tconst dx = colw + s.colspace // s.colspace may have been set to 0 by setAutoDimensions\n\tconst nx = this[`${col}s`].length\n\tconst dy = s.rowh + s.rowspace\n\tconst ny = this[`${row}s`].length\n\tconst mainwByColDimensions =\n\t\tnx * (colw + s.colspace) +\n\t\tthis[`${col}Grps`].length * s.colgspace +\n\t\t(this[`${col}s`].slice(-1)[0]?.totalHtAdjustments || 0)\n\tconst mainw = Math.min(mainwByColDimensions, this.availContentWidth)\n\n\tconst lastRow = this[`${row}s`].slice(-1)[0]\n\tconst mainh = ny * dy + (this[`${row}Grps`].length - 1) * s.rowgspace + (lastRow?.cumulativeAdjustment || 0)\n\n\tconst colLabelFontSize = Math.min(\n\t\tMath.max(colw + s.colspace - 2 * s.collabelpad - s.colspace, s.minLabelFontSize),\n\t\ts.maxLabelFontSize\n\t)\n\n\tconst topFontSize = _t_ == 'Grp' ? s.grpLabelFontSize : colLabelFontSize\n\tlayout.top.attr = {\n\t\tboxTransform: `translate(${xOffset}, ${yOffset - s.collabelgap})`,\n\t\tadjustBoxTransform: dx =>\n\t\t\tlayout.top.box.attr('transform', `translate(${xOffset + dx}, ${yOffset - s.collabelgap})`),\n\t\tlabelTransform: 'rotate(-90)',\n\t\tlabelAnchor: 'start',\n\t\tlabelGY: 0,\n\t\tlabelGTransform: this[`col${_t_}LabelGTransform`],\n\t\tfontSize: topFontSize,\n\t\ttextpos: { coord: 'y', factor: -1 },\n\t\taxisFxn: axisTop\n\t}\n\tif (layout.top.prefix == 'sample')\n\t\tlayout.top.display = s.sampleLabelsToggle !== 'hide' && colw >= s.minLabelFontSize ? '' : 'none'\n\n\tconst btmFontSize = _b_ == 'Grp' ? s.grpLabelFontSize : colLabelFontSize\n\tlayout.btm.attr = {\n\t\tboxTransform: `translate(${xOffset}, ${yOffset + mainh + s.collabelgap})`,\n\t\tadjustBoxTransform: dx =>\n\t\t\tlayout.btm.box.attr('transform', `translate(${xOffset + dx}, ${yOffset + mainh + s.collabelgap})`),\n\t\tlabelTransform: 'rotate(-90)',\n\t\tlabelAnchor: 'end',\n\t\tlabelGY: 0,\n\t\tlabelGTransform: this[`col${_b_}LabelGTransform`],\n\t\tfontSize: btmFontSize,\n\t\ttextpos: { coord: 'y', factor: 1 },\n\t\taxisFxn: axisBottom\n\t}\n\tif (layout.btm.prefix == 'sample')\n\t\tlayout.btm.display = s.sampleLabelsToggle !== 'hide' && colw >= s.minLabelFontSize ? '' : 'none'\n\n\tconst leftFontSize =\n\t\t_l_ == 'Grp'\n\t\t\t? s.grpLabelFontSize\n\t\t\t: Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad - s.rowspace, s.minLabelFontSize)\n\tlayout.left.attr = {\n\t\tboxTransform: `translate(${xOffset - s.rowlabelgap}, ${yOffset})`,\n\t\tlabelTransform: '',\n\t\tlabelAnchor: 'end',\n\t\tlabelGX: 0,\n\t\tlabelGTransform: this[`row${_l_}LabelGTransform`],\n\t\tfontSize: leftFontSize,\n\t\ttextpos: { coord: 'x', factor: -1 },\n\t\taxisFxn: axisLeft\n\t}\n\n\tconst rtFontSize =\n\t\t_r_ == 'Grp' ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad, s.minLabelFontSize)\n\tlayout.right.attr = {\n\t\tboxTransform: `translate(${xOffset + mainw + s.rowlabelgap}, ${yOffset})`,\n\t\tlabelTransform: '',\n\t\tlabelAnchor: 'start',\n\t\tlabelGX: 0,\n\t\tlabelGTransform: this[`row${_r_}LabelGTransform`],\n\t\tfontSize: rtFontSize,\n\t\ttextpos: { coord: 'x', factor: 1 },\n\t\taxisFxn: axisRight\n\t}\n\n\tthis.dom.sampleLabelsPG.attr('clip-path', s.transpose ? '' : `url(#${this.seriesClipId})`)\n\tthis.dom.termLabelsPG.attr('clip-path', s.transpose ? `url(#${this.seriesClipId})` : '')\n\n\tthis.layout = layout\n\tif (!s.zoomCenterPct) {\n\t\ts.zoomCenterPct = 0.5\n\t\ts.zoomIndex = Math.round((s.zoomCenterPct * mainw) / dx)\n\t\ts.zoomGrpIndex = this.sampleOrder[s.zoomIndex]?.grpIndex || 0\n\t}\n\t// zoomCenter relative to mainw\n\tconst zoomCenter = s.zoomCenterPct * mainw\n\tconst centerCellX = s.zoomIndex * dx + s.zoomGrpIndex * s.colgspace\n\tconst zoomedMainW = Math.max(0, nx * dx + (this[`${col}Grps`].length - 1) * s.colgspace)\n\tconst seriesXoffset =\n\t\ts.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : Math.max(zoomCenter - centerCellX, mainw - zoomedMainW)\n\n\t//\n\t// canvas-related dimensions, computed to not exceed an ultrawide, zoomed-in\n\t// image width limit that causes the canvas to not render, and also\n\t// the possibly narrowed image must be positioned correctly\n\t//\n\t// for a canvas-generated image, the image is sharper when the image width is not an integer,\n\t// so subtract a negligible decimal value to have a numeric real/float width value\n\tconst imgW = (s.imgWMax > zoomedMainW ? zoomedMainW : s.imgWMax) - 0.0000001\n\tconst halfImgW = 0.5 * imgW\n\t// determine how the canvas image will be offset relative to the center of mainw (the visible width)\n\tconst unwantedRightOvershoot = Math.max(0, centerCellX + halfImgW - zoomedMainW)\n\tconst imgLeftMin = Math.max(0, centerCellX - Math.min(halfImgW, imgW) - unwantedRightOvershoot)\n\t// canvas cells with x posistions that fall outside of xMin and xMax will not be rendered,\n\t// since they will be outside the computed allowed image width\n\tconst xMin = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : imgLeftMin\n\tconst xMax = imgW + xMin\n\t// console.log({ imgW, mainw, xMin, xMax, seriesXoffset, imgLeftMin, xOffset, centerCellX, zoomedMainW, imgWMax: s.imgWMax })\n\n\tthis.dimensions = {\n\t\txMin,\n\t\txMax,\n\t\tdx,\n\t\tdy,\n\t\txOffset,\n\t\tyOffset,\n\t\tmainw,\n\t\tmainh,\n\t\tcolw,\n\t\tzoomedMainW,\n\t\tseriesXoffset: seriesXoffset > 0 ? 0 : seriesXoffset,\n\t\tmaxMainW: Math.max(mainwByColDimensions, this.availContentWidth),\n\t\timgW,\n\t\t// recompute the resolvable \"pixel width\", in case the pixel ratio changes\n\t\t// when moving the browser window to a different monitor,\n\t\t// will be used to sharpen canvas shapes that are smaller than this pixel width\n\t\tpxw: 1 / window.devicePixelRatio\n\t}\n}\n"],
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+  "names": ["s", "dx"]
+}

package/dist/chunk-3AGB6HL4.js

@@ -0,0 +1,158 @@
+import {
+  appInit
+} from "./chunk-MXNSW55L.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-OXJ2TWDO.js";
+import {
+  mclass
+} from "./chunk-XYFDBYOY.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 5) {
+      errors.push("snv input not equal to 5 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-3AGB6HL4.js.map

package/dist/chunk-3AVDNIDN.js

@@ -0,0 +1,55 @@
+import {
+  colorinframe
+} from "./chunk-OXJ2TWDO.js";
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-XYFDBYOY.js";
+
+// src/spliceevent.phrase.js
+function spliceevent_phrase_default(evt) {
+  const htmls = [];
+  if (evt.isaltexon || evt.isskipexon) {
+    const exonstart = Math.min(...evt.skippedexon);
+    const exonstop = Math.max(...evt.skippedexon);
+    htmls.push(
+      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
+    );
+    if (evt.isaltexon) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
+      );
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
+    }
+    if (evt.junctionB.data) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
+      );
+    }
+    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
+    if (evt.framenocheck) {
+      if (evt.utr3) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
+      } else if (evt.utr5) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
+      }
+    } else if (evt.frame == IN_frame) {
+      htmls.push(
+        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
+      );
+    } else if (evt.frame == OUT_frame) {
+      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
+    }
+  } else {
+    return "unknown event type!!";
+  }
+  return htmls.join(" ");
+}
+
+export {
+  spliceevent_phrase_default
+};
+//# sourceMappingURL=chunk-3AVDNIDN.js.map