@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/chunk-D4QFQQWJ.js

@@ -0,0 +1,170 @@
+import {
+  getEmptyCell,
+  maySetEmptyCell,
+  setCellProps
+} from "./chunk-QMI222IJ.js";
+import {
+  TermTypeGroups
+} from "./chunk-XYFDBYOY.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.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);
+        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-D4QFQQWJ.js.map

package/dist/chunk-DNCSPTOQ.js

@@ -0,0 +1,446 @@
+import {
+  schemeCategory20
+} from "./chunk-V2OJLJSK.js";
+import {
+  isNumericTerm
+} from "./chunk-6ITDJ5UR.js";
+import {
+  dtcnv,
+  dtsnvindel
+} from "./chunk-XYFDBYOY.js";
+import {
+  category10_default
+} from "./chunk-IH7ILDJS.js";
+import {
+  linear,
+  ordinal
+} from "./chunk-OAWQ6LOO.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.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-DNCSPTOQ.js.map