@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/chunk-N2JOZ3QD.js

@@ -1,444 +0,0 @@
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  isNumericTerm
-} from "./chunk-QFQJO7LD.js";
-import {
-  category10_default,
-  dtcnv,
-  dtsnvindel
-} from "./chunk-2N345NXD.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-4OLM3KSB.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.legend.js
-var matrix_legend_exports = {};
-__export(matrix_legend_exports, {
-  CNVkey2order: () => CNVkey2order,
-  getLegendData: () => getLegendData,
-  getLegendItemText: () => getLegendItemText
-});
-function getLegendData(legendGroups, refs, self) {
-  const s = this.settings.matrix;
-  const legendData = [];
-  const dvt = this.config.divideBy || {};
-  const dvtId = dvt && "id" in dvt ? dvt.id : dvt.name;
-  for (const $id in legendGroups) {
-    const legend = legendGroups[$id];
-    if ($id == "Consequences") {
-      for (const f of this.config.legendValueFilter.lst) {
-        if (f.tvs.term.type !== "geneVariant") continue;
-        if (f.legendGrpName != $id) continue;
-        if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
-          continue;
-        }
-        for (const v of f.tvs.values) {
-          for (const key of v.mclasslst) {
-            const legendk = v.origin ? v.origin + key : key;
-            legend.values[legendk] = {
-              key,
-              dt: v.dt,
-              origin: v.origin,
-              label: v.label || self.mclass[key].label,
-              fill: v.color || self.mclass[key]?.color,
-              order: CNVkey2order(key),
-              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
-              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
-            };
-          }
-        }
-      }
-      const keys2 = Object.keys(legend.values);
-      if (!keys2.length) continue;
-      legendData.unshift({
-        name: "Consequences",
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        items: keys2.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          return {
-            termid: "Consequences",
-            key: item.key,
-            text: this.getLegendItemText(item, count, {}, s),
-            color: item.fill,
-            order: i,
-            border: "1px solid #ccc",
-            count,
-            isLegendItem: true,
-            dt: item.dt,
-            crossedOut: item.crossedOut,
-            greyedOut: item.greyedOut,
-            origin: item.origin
-          };
-        })
-      });
-      legendData[0].items.sort((a, b) => a.text < b.text ? -1 : 1);
-      continue;
-    }
-    const t = $id == dvtId ? { tw: dvt } : this.termOrder.find((t2) => t2.tw.$id == $id || t2.tw.legend?.group == $id) || {
-      tw: { term: { id: $id, name: $id, type: $id === "CNV" ? "geneVariant" : "" } }
-    };
-    for (const f of this.config.legendValueFilter.lst) {
-      const name = t.tw.legend?.group || t.tw.label || t.tw.term.name;
-      if (f.legendGrpName != $id && f.legendGrpName != name && f.tvs.term.name != name) continue;
-      if (f.tvs.term.type == "geneVariant") {
-        for (const v of f.tvs.values) {
-          if (legend.dt && !legend.dt.includes(v.dt)) legend.dt.push(v.dt);
-          if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
-            continue;
-          }
-          for (const key of v.mclasslst) {
-            const legendk = v.origin ? v.origin + key : key;
-            legend.values[legendk] = {
-              key,
-              dt: v.dt,
-              origin: v.origin,
-              label: v.label || self.mclass[key]?.label || "Gain and loss",
-              fill: v.color || self.mclass[key]?.color,
-              order: CNVkey2order(key),
-              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
-              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
-            };
-          }
-        }
-      } else {
-        if (isNumericTerm(f.tvs.term)) {
-          if (t.ref?.bins) {
-            for (const v of f.tvs.ranges) {
-              const termValues = t.ref.bins;
-              legend.values[v.name] = {
-                key: v.name,
-                label: termValues?.find((vl) => vl.name == v.name)?.name || v.name,
-                fill: termValues?.find((vl) => vl.name == v.name)?.color,
-                crossedOut: true
-              };
-            }
-          }
-        } else if (f.tvs.term.type == "survival") {
-          for (const v of f.tvs.values) {
-            const termValues = t.tw.term.values;
-            legend.values[v.key] = {
-              key: v.key,
-              label: termValues?.[v.key]?.label || "Exit code: " + v.key,
-              fill: v.key == 1 ? "#ff7f0e" : "#1f77b4",
-              crossedOut: true
-            };
-          }
-        } else {
-          for (const v of f.tvs.values) {
-            const termValues = t.tw.term.values;
-            legend.values[v.key] = {
-              key: v.key,
-              label: termValues?.[v.key]?.label || v.key,
-              fill: termValues?.[v.key]?.color,
-              crossedOut: true
-            };
-          }
-        }
-      }
-    }
-    const keys = Object.keys(legend.values).sort();
-    const hasScale = Object.values(legend.values).find((v) => v.scale);
-    if (hasScale) {
-      if (legend === legendGroups?.CNV) {
-        const gain = legend.values["CNV_amp"];
-        const loss = legend.values["CNV_loss"];
-        if (gain?.scale && loss?.scale) {
-          const colors = loss.scales?.legend.range;
-          const domain = loss.scales?.legend.domain;
-          const setLegendAttr = (item) => {
-            return {
-              $id,
-              domain: item.scales.legend.domain,
-              key: item.key,
-              isLegendItem: true,
-              minLabel: domain[0],
-              //item.minLoss, // item.maxLabel,
-              maxLabel: domain.slice(-1)[0],
-              //item.maxGain, // item.maxLabel,
-              scale: item.scale,
-              termid: "CNV"
-            };
-          };
-          const numericInputs = {
-            cutoffMode: s.cnvValues.cutoffMode,
-            defaultPercentile: s.cnvValues.defaultPercentile,
-            percentile: s.cnvValues.percentile,
-            callback: async (obj) => {
-              const cValues = self.config.settings.matrix.cnvValues;
-              if (obj.cutoffMode == "fixed") {
-                if (cValues.min == null) cValues.min = domain[0];
-                if (cValues.max == null) cValues.max = domain[domain.length - 1];
-                if (obj.min != cValues.min) obj.max = Math.abs(obj.min);
-                else obj.min = -obj.max;
-              }
-              self.config.settings.matrix.cnvValues = {
-                defaultPercentile: self.config.settings.matrix.cnvValues.defaultPercentile,
-                cutoffMode: obj.cutoffMode,
-                min: obj.min,
-                max: obj.max,
-                percentile: obj.percentile
-              };
-              await self.app.dispatch({
-                type: "plot_edit",
-                id: self.opts.id,
-                config: self.config
-              });
-            }
-          };
-          legend.values.CNV_gain_loss = {
-            key: $id,
-            label: "Gain and Loss",
-            dt: dtcnv,
-            order: -1,
-            domain,
-            name: "CNV gain/loss",
-            scale: linear().domain(domain).range(colors),
-            scales: loss.scales,
-            //Prevent the colors and domain recalculating below
-            minLabel: domain[0],
-            //loss.maxLabel,
-            maxLabel: domain.slice(-1)[0],
-            labels: { left: "Loss", right: "Gain" },
-            parents: [Object.assign(setLegendAttr(loss), loss), Object.assign(setLegendAttr(gain), gain)],
-            samples: /* @__PURE__ */ new Set([...gain.samples, ...loss.samples]),
-            numericInputs
-          };
-          delete legend.values[gain.key];
-          delete legend.values[loss.key];
-          keys.splice(keys.indexOf(gain.key), 1);
-          keys.splice(keys.indexOf(loss.key), 1);
-          keys.push("CNV_gain_loss");
-        }
-      }
-      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
-      legendData.push({
-        name: $id.length < legendGrpLabelMaxChars ? $id : $id.slice(0, legendGrpLabelMaxChars) + "...",
-        //name:$id,
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        hasScale,
-        items: keys.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          if (item.scale) {
-            const colors = item.scales?.legend?.range || getColors(item);
-            const domain = item.scales?.legend?.domain || setColorScaleDomain(item.minLabel, item.maxLabel, item.domain, colors);
-            const opts = {
-              termid: $id,
-              key: item.key,
-              text: this.getLegendItemText(item, count, t, s),
-              width: 100,
-              scale: item.scale,
-              colors,
-              domain,
-              order: "order" in item ? item.order : i,
-              count,
-              isLegendItem: true,
-              dt: item.dt,
-              crossedOut: item.crossedOut,
-              greyedOut: item.greyedOut,
-              origin: item.origin,
-              parents: item.parents,
-              labels: item.labels
-            };
-            if (item.numericInputs) {
-              opts.numericInputs = item.numericInputs;
-            }
-            return opts;
-          } else {
-            return {
-              termid: $id,
-              key: item.key,
-              text: this.getLegendItemText(item, count, t, s),
-              color: item.fill || this.colorScaleByTermId[$id](key),
-              order: "order" in item ? item.order : i,
-              count,
-              isLegendItem: true,
-              dt: item.dt,
-              crossedOut: item.crossedOut,
-              greyedOut: item.greyedOut,
-              origin: item.origin
-            };
-          }
-        })
-      });
-    } else {
-      const grp = $id;
-      const term = t.tw.term;
-      const ref = legend.ref;
-      if (ref.bins)
-        keys.sort((a, b) => ref.bins.findIndex((bin) => bin.name === a) - ref.bins.findIndex((bin) => bin.name === b));
-      else if (ref.keyOrder) keys.sort((a, b) => ref.keyOrder.indexOf(a) - ref.keyOrder.indexOf(b));
-      if (!this.colorScaleByTermId[grp])
-        this.colorScaleByTermId[grp] = keys.length < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
-      const name = t.tw.legend?.group || t.tw.label || term.name;
-      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
-      legendData.push({
-        name: name.length < legendGrpLabelMaxChars ? name : name.slice(0, legendGrpLabelMaxChars) + "...",
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        items: keys.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          return {
-            $id,
-            termid: term.id || term.name,
-            key: item.key,
-            text: this.getLegendItemText(item, count, t, s),
-            color: t.scale || item.fill || this.colorScaleByTermId[grp](key),
-            order: "order" in item ? item.order : i,
-            count,
-            isExcluded: item.isExcluded,
-            //onClickCallback: this.handleLegendItemClick,
-            isLegendItem: true,
-            dt: item.dt,
-            crossedOut: item.crossedOut,
-            greyedOut: item.greyedOut,
-            origin: item.origin
-          };
-        })
-      });
-    }
-  }
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 4 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 4)) {
-      legendData.push({
-        name: "CNV",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 4,
-            termid: "CNV",
-            origin: grpFilter.origin,
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    } else if (grpFilter.dt.includes(dtsnvindel)) {
-      const controlLabels = self.settings.matrix.controlLabels;
-      const groupName = grpFilter.origin ? `${grpFilter.origin[0].toUpperCase() + grpFilter.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations;
-      if (!legendData.filter((l) => l.dt)?.find((l) => l.dt.includes(dtsnvindel) && l.origin == grpFilter.origin)) {
-        legendData.push({
-          name: groupName,
-          dt: grpFilter.dt,
-          origin: grpFilter.origin,
-          crossedOut: true,
-          items: grpFilter.filteredOutCats.map((fc) => {
-            return {
-              dt: self.mclass[fc].dt,
-              origin: grpFilter.origin,
-              termid: groupName,
-              key: fc,
-              text: self.mclass[fc].label,
-              color: self.mclass[fc]?.color,
-              isLegendItem: true
-            };
-          })
-        });
-      }
-    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 2 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 2)) {
-      legendData.push({
-        name: "Fusion RNA",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 2,
-            origin: grpFilter.origin,
-            termid: "Fusion RNA",
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 5 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 5)) {
-      legendData.push({
-        name: "Structural Variation",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 5,
-            origin: grpFilter.origin,
-            termid: "Structural Variation",
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    }
-  }
-  for (const itemsGrp of legendData) {
-    itemsGrp.items.sort((a, b) => {
-      const getStatusOrder = (item) => {
-        if (!item.greyedOut && !item.crossedOut) return 0;
-        if (item.greyedOut && !item.crossedOut) return 1;
-        if (item.crossedOut) return 2;
-        return 3;
-      };
-      return getStatusOrder(a) - getStatusOrder(b);
-    });
-  }
-  return legendData.sort(
-    (a, b) => a.crossedOut && b.crossedOut ? 0 : a.crossedOut ? 1 : b.crossedOut ? -1 : a.order && b.order ? a.order - b.order : a.order ? -1 : b.order ? 1 : 0
-  );
-}
-function getLegendItemText(item, count, t, s) {
-  if (item.crossedOut || item.greyedOut) {
-    return item.label;
-  }
-  let text = item.label;
-  const notes = [count];
-  if (item.isExcluded) notes.push("hidden");
-  if (t?.tw?.term?.type == "geneVariant" && s.geneVariantCountSamplesSkipMclass.includes(item.key))
-    notes.push("not counted");
-  if (!notes.length) return text;
-  return text += ` (${notes.join(", ")})`;
-}
-function setColorScaleDomain(min, max, domain, colors) {
-  if (domain[0] === min && domain[domain.length - 1] === max) return domain;
-  const step = (max - min) / (colors.length - 1);
-  return colors.map((_, i) => {
-    if (i === (colors.length - 1) / 2 && min < 0 && max > 0) return 0;
-    return min + step * i;
-  });
-}
-function getColors(item) {
-  return item.domain?.map((c) => item.scale(c)) || item.scale.range();
-}
-function CNVkey2order(key) {
-  return key == "CNV_homozygous_deletion" ? -5 : key == "CNV_amplification" ? -4 : key == "CNV_loss" ? -3 : key == "CNV_amp" ? -2 : key == "CNV_loh" ? -1 : 0;
-}
-
-export {
-  getLegendData,
-  getLegendItemText,
-  CNVkey2order,
-  matrix_legend_exports
-};
-//# sourceMappingURL=chunk-N2JOZ3QD.js.map

package/dist/chunk-NG2U3VHX.js

@@ -1,170 +0,0 @@
-import {
-  getEmptyCell,
-  maySetEmptyCell,
-  setCellProps
-} from "./chunk-CHQ43UJQ.js";
-import {
-  TermTypeGroups
-} from "./chunk-2N345NXD.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.serieses.js
-var matrix_serieses_exports = {};
-__export(matrix_serieses_exports, {
-  getSerieses: () => getSerieses
-});
-function getSerieses(data) {
-  const s = this.settings.matrix;
-  const serieses = [];
-  const { colw, dx, dy, xMin, xMax } = this.dimensions;
-  const dvt = this.config.divideBy || {};
-  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
-  const legendGroups = {};
-  this.colorScaleByTermId = {};
-  for (const t of this.termOrder) {
-    const $id = t.tw.$id;
-    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
-    const isDivideByTerm = termid === divideByTermId;
-    const emptyGridCells = [];
-    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
-    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
-    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
-    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
-    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
-    const series = {
-      t,
-      tw: t.tw,
-      cells: [],
-      y,
-      hoverY0,
-      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
-    };
-    for (const so of this.unfilteredSampleOrder) {
-      const { totalIndex, grpIndex, row } = so;
-      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
-      const anno = row[$id];
-      const cellTemplate = {
-        s: so,
-        sample: row.sample,
-        tw: t.tw,
-        term: t.tw.term,
-        termid,
-        $id,
-        totalIndex,
-        grpIndex,
-        row,
-        t,
-        seriesY: y
-      };
-      if (!anno) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      const key = anno.key;
-      const values = anno.filteredValues || anno.values || [anno.value];
-      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
-      const height = !s.transpose ? s.rowh / numRects : colw;
-      const width = !s.transpose ? colw : colw / values.length;
-      const siblingCells = [];
-      if (!anno || !anno.renderedValues?.length) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      for (const [i, value] of values.entries()) {
-        const cell = Object.assign({ key, siblingCells }, cellTemplate);
-        cell.valueIndex = i;
-        let legend;
-        if (typeof t.tw.setCellProps == "function") {
-          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
-        } else {
-          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
-          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
-        }
-        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
-        if (legend) {
-          for (const l of [legendGroups, so.grp.legendGroups]) {
-            if (!l) continue;
-            if (!l[legend.group]) {
-              l[legend.group] = {
-                ref: legend.ref,
-                values: {},
-                order: legend.order,
-                $id,
-                origin: legend.entry.origin
-              };
-              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
-            }
-            const lg = l[legend.group];
-            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
-            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
-            if (!lg.values[legendK]) {
-              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
-              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
-            }
-            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
-            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
-              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
-            } else lg.values[legendK].samples.add(row.sample);
-            if (isDivideByTerm) {
-              lg.values[legend.value].isExcluded = so.grp.isExcluded;
-            }
-          }
-        }
-        if (!so.grp.isExcluded) {
-          if (anno.renderedValues.includes(value)) series.cells.push(cell);
-          siblingCells.push(cell);
-        }
-      }
-      if (s.showGrid == "rect" && !so.grp.isExcluded) {
-        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
-        if (cell) emptyGridCells.push(cell);
-      }
-    }
-    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
-    if (series.cells.length) serieses.push(series);
-  }
-  addAllHiddenLegendGroups(legendGroups, this);
-  this.legendData = this.getLegendData(legendGroups, data.refs, this);
-  for (const grp of this.sampleGroups) {
-    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
-  }
-  return serieses;
-}
-function addAllHiddenLegendGroups(legendGroups, self) {
-  for (const valueFilter of self.config.legendValueFilter.lst) {
-    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
-      legendGroups[valueFilter.legendGrpName] = {
-        ref: {},
-        values: {},
-        dt: [valueFilter.tvs.values[0].dt],
-        origin: valueFilter.tvs.values[0].origin
-      };
-    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    }
-  }
-}
-
-export {
-  getSerieses,
-  matrix_serieses_exports
-};
-//# sourceMappingURL=chunk-NG2U3VHX.js.map