@sjcrh/proteinpaint-client 2.146.4-1 → 2.147.1

package/dist/matrix.interactivity-PLS5VRBD.js

@@ -0,0 +1,35 @@
+import {
+  getConfigForShowAll,
+  setInteractivity,
+  showAll
+} from "./chunk-34NFZDPP.js";
+import "./chunk-5GYHGTRN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-BX6ANKGQ.js";
+import "./chunk-4JXJ4UBP.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-RY7CVONT.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-EUFBKP6Q.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-4W3BORF5.js";
+import "./chunk-SU6RBYZK.js";
+import "./chunk-2J7NXRQQ.js";
+import "./chunk-IVJWQYGG.js";
+import "./chunk-OMO754MK.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getConfigForShowAll,
+  setInteractivity,
+  showAll
+};
+//# sourceMappingURL=matrix.interactivity-PLS5VRBD.js.map

package/dist/matrix.layout-CIWDTBWE.js

@@ -0,0 +1,37 @@
+import {
+  getMaxGrpLabelWidth,
+  setAutoDimensions,
+  setLabelsAndScales,
+  setLayout
+} from "./chunk-PGNZXLHB.js";
+import "./chunk-5GYHGTRN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-BX6ANKGQ.js";
+import "./chunk-4JXJ4UBP.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-RY7CVONT.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-EUFBKP6Q.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-4W3BORF5.js";
+import "./chunk-SU6RBYZK.js";
+import "./chunk-2J7NXRQQ.js";
+import "./chunk-IVJWQYGG.js";
+import "./chunk-OMO754MK.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getMaxGrpLabelWidth,
+  setAutoDimensions,
+  setLabelsAndScales,
+  setLayout
+};
+//# sourceMappingURL=matrix.layout-CIWDTBWE.js.map

package/dist/matrix.legend-GEBKE674.js

@@ -0,0 +1,22 @@
+import {
+  CNVkey2order,
+  getLegendData,
+  getLegendItemText
+} from "./chunk-5U3ZO5HT.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  CNVkey2order,
+  getLegendData,
+  getLegendItemText
+};
+//# sourceMappingURL=matrix.legend-GEBKE674.js.map

package/dist/matrix.renderers-DDZYFY3A.js

@@ -0,0 +1,31 @@
+import {
+  setRenderers
+} from "./chunk-CFQQBWWZ.js";
+import "./chunk-5GYHGTRN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-BX6ANKGQ.js";
+import "./chunk-4JXJ4UBP.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-RY7CVONT.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-EUFBKP6Q.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-4W3BORF5.js";
+import "./chunk-SU6RBYZK.js";
+import "./chunk-2J7NXRQQ.js";
+import "./chunk-IVJWQYGG.js";
+import "./chunk-OMO754MK.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  setRenderers
+};
+//# sourceMappingURL=matrix.renderers-DDZYFY3A.js.map

package/dist/matrix.serieses-43Y763CP.js

@@ -0,0 +1,21 @@
+import {
+  getSerieses
+} from "./chunk-LZEQJFZ3.js";
+import "./chunk-K6HYNIAS.js";
+import "./chunk-5U3ZO5HT.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getSerieses
+};
+//# sourceMappingURL=matrix.serieses-43Y763CP.js.map

package/dist/matrix.sort-Y4NQ3QL2.js

@@ -0,0 +1,27 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getSortOptions,
+  getTermSorter,
+  reshapeSortPriority
+} from "./chunk-XT4XFXJW.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getSortOptions,
+  getTermSorter,
+  reshapeSortPriority
+};
+//# sourceMappingURL=matrix.sort-Y4NQ3QL2.js.map

package/dist/matrix.sort.unit.spec-VU3JMF2L.js

@@ -0,0 +1,465 @@
+import {
+  getPlotConfig
+} from "./chunk-CRH6WHU2.js";
+import {
+  getSampleSorter,
+  getSortOptions
+} from "./chunk-XT4XFXJW.js";
+import {
+  require_tape
+} from "./chunk-EFPC6YYT.js";
+import "./chunk-5GYHGTRN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-BX6ANKGQ.js";
+import "./chunk-4JXJ4UBP.js";
+import "./chunk-4YNEZISK.js";
+import "./chunk-RY7CVONT.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-EUFBKP6Q.js";
+import {
+  CNVClasses,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-PAV653SV.js";
+import "./chunk-4W3BORF5.js";
+import "./chunk-SU6RBYZK.js";
+import "./chunk-2J7NXRQQ.js";
+import "./chunk-IVJWQYGG.js";
+import "./chunk-OMO754MK.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/test/matrix.sort.unit.spec.js
+var import_tape = __toESM(require_tape(), 1);
+var terms = {
+  aaa: { name: "aaa", type: "geneVariant" },
+  bbb: { name: "bbb", type: "geneVariant" },
+  ccc: { name: "ccc", type: "geneVariant" }
+};
+async function getArgs(_settings = {}) {
+  const samples = {
+    1: {
+      sample: 1,
+      bbb: {
+        values: [{ dt: 1, class: "M" }]
+      },
+      ccc: {
+        values: [{ dt: 1, class: "M" }]
+      }
+    },
+    2: {
+      sample: 2,
+      aaa: {
+        values: [{ dt: 1, class: "M" }]
+      },
+      bbb: {
+        values: [{ dt: 1, class: "M" }]
+      }
+    },
+    3: {
+      sample: 3,
+      aaa: {
+        values: [
+          { dt: 1, class: "F" },
+          { dt: 4, class: "CNV_loss" }
+        ]
+      },
+      ccc: {
+        values: [{ dt: 1, class: "M" }]
+      }
+    },
+    4: {
+      sample: 4,
+      ccc: {
+        values: [{ dt: 1, class: "M" }]
+      }
+    },
+    5: {
+      sample: 5,
+      aaa: {
+        values: [{ dt: 1, class: "M" }]
+      },
+      bbb: {
+        values: [{ dt: 1, class: "M" }]
+      }
+    }
+  };
+  const sg = [
+    {
+      name: "Sample Group 1",
+      lst: [samples["1"], samples["2"], samples["3"]]
+    },
+    {
+      name: "Sample Group 2",
+      lst: [samples["4"], samples["5"]]
+    }
+  ];
+  const tg = [
+    {
+      name: "Term Group 1",
+      lst: [
+        { $id: "aaa", term: terms.aaa },
+        { $id: "bbb", term: terms.bbb },
+        { $id: "ccc", term: terms.ccc }
+      ]
+    }
+  ];
+  const app = { vocabApi: { termdbConfig: {} } };
+  const config = await getPlotConfig(
+    {
+      settings: {
+        matrix: {
+          sortSamplesTieBreakers: [{ $id: "sample", sortSamples: { by: "sample" } }],
+          sortByMutation: "presence",
+          sortByCNV: false,
+          hiddenVariants: [],
+          proteinChangingMutations,
+          truncatingMutations,
+          synonymousMutations,
+          mutationClasses,
+          CNVClasses,
+          ..._settings
+        }
+      }
+    },
+    app
+  );
+  const settings = config.settings;
+  config.sortOptions = getSortOptions(void 0, void 0, settings.matrix);
+  const rows = Object.values(samples);
+  return {
+    self: {
+      app,
+      config,
+      termGroups: tg,
+      sampleGroups: sg,
+      sampleOrder: [
+        {
+          grp: sg[0],
+          grpIndex: 0,
+          index: sg[0].lst.findIndex((s) => s.sample === 1),
+          row: samples["1"]
+        },
+        {
+          grp: sg[0],
+          grpIndex: 0,
+          index: sg[0].lst.findIndex((s) => s.sample === 2),
+          row: samples["2"]
+        },
+        {
+          grp: sg[0],
+          grpIndex: 0,
+          index: sg[0].lst.findIndex((s) => s.sample === 3),
+          row: samples["3"]
+        },
+        {
+          grp: sg[1],
+          grpIndex: 1,
+          index: sg[1].lst.findIndex((s) => s.sample === 4),
+          row: samples["4"]
+        },
+        {
+          grp: sg[1],
+          grpIndex: 1,
+          index: sg[1].lst.findIndex((s) => s.sample === 5),
+          row: samples["5"]
+        }
+      ],
+      termOrder: [
+        {
+          grp: tg[0],
+          grpIndex: 0,
+          counts: rows.filter((r) => "aaa" in r).length,
+          index: tg[0].lst.findIndex((tw) => tw.term.name == "aaa"),
+          tw: tg[0].lst.find((tw) => tw.term.name == "aaa")
+        },
+        {
+          grp: tg[0],
+          grpIndex: 0,
+          counts: rows.filter((r) => "bbb" in r).length,
+          index: tg[0].lst.findIndex((tw) => tw.term.name == "bbb"),
+          tw: tg[0].lst.find((tw) => tw.term.name == "bbb")
+        },
+        {
+          grp: tg[0],
+          grpIndex: 0,
+          counts: rows.filter((r) => "ccc" in r).length,
+          index: tg[0].lst.findIndex((tw) => tw.term.name == "ccc"),
+          tw: tg[0].lst.find((tw) => tw.term.name == "ccc")
+        }
+      ]
+    },
+    settings: settings.matrix,
+    rows: Object.values(samples)
+  };
+}
+function simpleMatrix(sampleNames, termOrder, rows) {
+  const lst = [];
+  for (const sn of sampleNames) lst.push(...sn);
+  rows.sort((a, b) => lst.indexOf(a.sample) - lst.indexOf(b.sample));
+  const matrix = termOrder.map(() => []);
+  for (const r of rows) {
+    for (const [i, m] of matrix.entries()) {
+      m.push(termOrder[i].tw.$id in r ? `${r.sample}` : " ");
+    }
+  }
+  return matrix;
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/matrix.sort -***-");
+  test.end();
+});
+(0, import_tape.default)("sortSamplesBy = asListed", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({ sortSamplesBy: "asListed" });
+  self.asListedSampleOrder = [1, 2, 3, 4, 5];
+  const sorter = getSampleSorter(self, settings, rows);
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      [1, 2, 3],
+      [4, 5]
+    ],
+    "should sort the samples as listed"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      [" ", "2", "3", " ", "5"],
+      ["1", "2", " ", " ", "5"],
+      ["1", " ", "3", "4", " "]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+(0, import_tape.default)("sortPriority by Mutation categories, default no value sorting, that uses a filter", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({
+    sortSamplesBy: "a"
+  });
+  const sorter = getSampleSorter(self, settings, rows);
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      // NOTE on 5/29/2024:
+      // When prioritizing truncating mutations, samples with F (truncating)
+      // will be sorted before samples with only M (non-truncating)
+      // for a given gene row
+      [3, 2, 1],
+      [5, 4]
+    ],
+    "should sort the samples by dt then value"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      ["3", "2", " ", "5", " "],
+      [" ", "2", "1", "5", " "],
+      ["3", " ", "1", " ", "4"]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+(0, import_tape.default)("sortPriority by Mutation categories with value sorting, that uses a filter", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({
+    sortSamplesBy: "a",
+    showMatrixMutation: "onlyPC",
+    showMatrixCNV: "all"
+  });
+  const tb = settings.sortOptions.a.sortPriority[0].tiebreakers[2];
+  tb.disabled = false;
+  tb.isOrdered = true;
+  const sorter = getSampleSorter(self, settings, rows);
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      [3, 2, 1],
+      [5, 4]
+    ],
+    "should sort the samples by dt then value"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      ["3", "2", " ", "5", " "],
+      [" ", "2", "1", "5", " "],
+      ["3", " ", "1", " ", "4"]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+(0, import_tape.default)("custom sortPriority, without filter", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({
+    sortSamplesBy: "custom",
+    sortOptions: {
+      custom: {
+        value: "custom",
+        sortPriority: [
+          {
+            types: ["geneVariant"],
+            tiebreakers: [
+              {
+                by: "dt",
+                order: [1]
+                // snvindel, cnv,
+                // other dt values will be ordered last
+                // for the sorter to not consider certain dt values,
+                // need to explicitly not use such values for sorting
+                // ignore: [4]
+              },
+              {
+                by: "class",
+                order: [
+                  // truncating
+                  "F",
+                  "N",
+                  // indel
+                  "D",
+                  "I",
+                  // point
+                  "M",
+                  "P",
+                  "L",
+                  // noncoding
+                  "Utr3",
+                  "Utr5",
+                  "S",
+                  "Intron"
+                ]
+              }
+            ]
+          },
+          {
+            types: ["geneVariant"],
+            tiebreakers: [
+              {
+                by: "dt",
+                order: [4]
+                // snvindel, cnv,
+                // other dt values will be ordered last
+                // for the sorter to not consider certain dt values,
+                // need to explicitly not use such values for sorting
+                // ignore: [4]
+              },
+              {
+                by: "class",
+                order: [
+                  // Lou and JZ wanted samples with CNV to be sorted first??
+                  "CNV_loss",
+                  "CNV_amp"
+                ]
+              }
+            ]
+          }
+        ]
+      }
+    }
+  });
+  const sorter = getSampleSorter(self, settings, rows);
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      [3, 2, 1],
+      [5, 4]
+    ],
+    "should sort the samples by dt then value"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      ["3", "2", " ", "5", " "],
+      [" ", "2", "1", "5", " "],
+      ["3", " ", "1", " ", "4"]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+(0, import_tape.default)("sort against selectedTerms", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({ sortSamplesBy: "dt" });
+  self.termGroups[0].lst[1].sortSamples = {};
+  settings.sortSamplesBy = "a";
+  const sorter = getSampleSorter(self, settings, rows);
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      [2, 1, 3],
+      [5, 4]
+    ],
+    "should sort the samples by dt-only"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      ["2", " ", "3", "5", " "],
+      ["2", "1", " ", "5", " "],
+      [" ", "1", "3", " ", "4"]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+(0, import_tape.default)("getSampleSorter() should apply an opts.skipSorter() argument", async (test) => {
+  test.timeoutAfter(1e3);
+  test.plan(2);
+  const { self, settings, rows } = await getArgs({
+    sortSamplesBy: "a"
+  });
+  const sorter = getSampleSorter(self, settings, rows, {
+    skipSorter: (p, tw) => tw.term.name == "aaa"
+  });
+  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
+  test.deepEqual(
+    sampleNames,
+    [
+      [1, 2, 3],
+      [5, 4]
+    ],
+    "should sort the samples by dt then value"
+  );
+  test.deepEqual(
+    simpleMatrix(sampleNames, self.termOrder, rows),
+    // prettier-ignore
+    [
+      [" ", "2", "3", "5", " "],
+      ["1", "2", " ", "5", " "],
+      ["1", " ", "3", " ", "4"]
+    ],
+    "should sort sample and rows in the expected order"
+  );
+  test.end();
+});
+//# sourceMappingURL=matrix.sort.unit.spec-VU3JMF2L.js.map

package/dist/matrix.sorterUi-47XHMDWW.js

@@ -0,0 +1,18 @@
+import {
+  getSorterUi
+} from "./chunk-7FDVPL6E.js";
+import "./chunk-PAV653SV.js";
+import "./chunk-SU6RBYZK.js";
+import "./chunk-IVJWQYGG.js";
+import "./chunk-PMZS3SHH.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-W2IWHXLL.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getSorterUi
+};
+//# sourceMappingURL=matrix.sorterUi-47XHMDWW.js.map