@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/matrix.integration.spec-2N237E7T.js

@@ -0,0 +1,3156 @@
+import {
+  getSortOptions
+} from "./chunk-5DI4UNH5.js";
+import "./chunk-C2MCQZWH.js";
+import {
+  getRunPp
+} from "./chunk-2SL4QWUS.js";
+import {
+  detectLst,
+  sleep
+} from "./chunk-WA3C3A2M.js";
+import {
+  termjson
+} from "./chunk-CWWE77DH.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-PRTLCJYF.js";
+import "./chunk-THAUD62Q.js";
+import "./chunk-5AXS5G4A.js";
+import "./chunk-MXKYPTZ7.js";
+import "./chunk-O6T4SDC7.js";
+import "./chunk-HH3NUAR2.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-VLIOMJDR.js";
+import "./chunk-K3G56J5R.js";
+import "./chunk-WD7FZ5EE.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-WXSMUSU7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  CNVClasses,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/test/matrix.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/matrix -***-");
+  test.end();
+});
+(0, import_tape.default)("only dictionary terms", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(5);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "sex"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                  // or 'continuous'
+                },
+                {
+                  id: "Arrhythmias"
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      240,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const sg0rects = matrix.Inner.dom.seriesesG.select(".sjpp-mass-series-g").selectAll("rect");
+    test.equal(
+      sg0rects.filter((d) => d.key <= 0 && d.fill === "transparent").size(),
+      14,
+      `should render special values with transparent rects`
+    );
+    const uniqueHts = /* @__PURE__ */ new Set();
+    sg0rects.each((d) => uniqueHts.add(d.height));
+    test.equal(uniqueHts.size, 45, `should render different rect heights for continuous mode bar plots`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("termCollection", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          termgroups: [
+            {
+              name: "",
+              lst: [getTermCollection()]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: { callbacks: { "postRender.test": runTests } }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("with divide by terms", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "sex"
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                { id: "agedx", term: termjson["agedx"] },
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      180,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      2,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("long column group labels", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "diaggrp"
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "agedx", term: termjson["agedx"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test222": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test222", null);
+    const y = matrix.Inner.dom.clipRect.property("y").baseVal.value;
+    test.true(y > -63 && y < -62, `should adjust the clip-path rect y-value to between -39 and -38, actual=${y}`);
+    const h = matrix.Inner.dom.clipRect.property("height").baseVal.value;
+    test.true(h > 619 && h <= 620, `should adjust the clip-path height to between 595 and 596, actual=${h}`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("divide by continuous terms", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "agedx"
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                { id: "sex", term: termjson["sex"] },
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      180,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      5,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("geneVariant term", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [{ term: { gene: "TP53", name: "TP53", type: "geneVariant", isleaf: true } }]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      242,
+      `should render the expected number of cell rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("geneVariant terms and dictionary terms", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                ...getGenes(),
+                { id: "agedx", term: termjson["agedx"] },
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      6,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      902,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("geneVariant terms with divide by dictionary term", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "sex"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      752,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      2,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("geneVariant terms and dictionary terms divide by dictionary term", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "sex"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                ...getGenes(),
+                { id: "agedx", term: termjson["agedx"] },
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      6,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      962,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      2,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort samples by sample name", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(4);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSamplesBy: "name"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const g = matrix.Inner.dom.sampleLabelsPG.selectAll(".sjpp-matrix-series-label-g g");
+    test.equal(g.size(), 60, `should render the expected number of sample names`);
+    test.equal(g._groups[0][0].textContent, "2646", `should be the expected sample name`);
+    test.equal(g._groups[0][9].textContent, "2772", `should be the expected sample name`);
+    test.equal(g._groups[0][59].textContent, "3472", `should be the expected sample name`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort samples by Mutation categories, not sorted by CNV", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(4);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSamplesBy: "a"
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.sampleLabelsPG.selectAll(".sjpp-matrix-series-label-g g").size(),
+      60,
+      `should render the expected number of sample names`
+    );
+    const rects = matrix.Inner.dom.sampleLabelsPG.selectAll(".sjpp-matrix-series-label-g g")._groups[0];
+    const index_3346 = Array.from(rects).find((rect) => rect.textContent == "3346").__data__.index;
+    test.true(index_3346 < 10, `sample 3346 should be in the expected order (not sorted by CNV)`);
+    const index_2660 = Array.from(rects).find((rect) => rect.textContent == "2660").__data__.index;
+    test.equal(index_2660, 8, `sample 2660 should be in the expected order (not sorted by CNV)`);
+    const index_3472 = Array.from(rects).find((rect) => rect.textContent == "3472").__data__.index;
+    test.true(index_3472 > 9, `sample 3472 should be in the expected order (not sorted by CNV)`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort samples by CNV+SSM > SSM-only", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(5);
+  const sortOptions = getSortOptions(
+    void 0,
+    {},
+    {
+      proteinChangingMutations,
+      truncatingMutations,
+      synonymousMutations,
+      mutationClasses,
+      CNVClasses
+    }
+  );
+  const cnvtb = sortOptions.a.sortPriority[0].tiebreakers[2];
+  cnvtb.disabled = false;
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          legendValueFilter: {
+            type: "tvslst",
+            lst: []
+          },
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSamplesBy: "a",
+              sortOptions
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.sampleLabelsPG.selectAll(".sjpp-matrix-series-label-g g").size(),
+      60,
+      `should render the expected number of sample names`
+    );
+    const rects = matrix.Inner.dom.sampleLabelsPG.selectAll(".sjpp-matrix-series-label-g g")._groups[0];
+    const r = Array.from(rects);
+    const index_3416 = r.find((rect) => rect.textContent == "3416").__data__.index;
+    test.equal(index_3416, 0, `should be in the expected order`);
+    const index_3346 = r.find((rect) => rect.textContent == "3346").__data__.index;
+    test.equal(index_3346, 9, `should be in the expected order`);
+    const index_2660 = r.find((rect) => rect.textContent == "2660").__data__.index;
+    test.equal(index_2660, 11, `should be in the expected order`);
+    const index_3472 = r.find((rect) => rect.textContent == "3472").__data__.index;
+    test.equal(index_3472, r.length - 1, `should be in the expected order`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("set max number of samples", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(1);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200,
+              maxSample: 10
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  id: "sex"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      10,
+      `should render the expected number of cell rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort sample groups by Group Name", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSampleGrpsBy: "name"
+            }
+          },
+          divideBy: {
+            id: "genetic_race"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const matrixGroupLabels = matrix.Inner.dom.sampleLabelsPG.selectAll(
+      ".sjpp-matrix-series-group-label-g .sjpp-matrix-label"
+    )._groups[0];
+    test.true(matrixGroupLabels[0].textContent.startsWith("African Ancestry"), `should be the expected group name`);
+    test.true(matrixGroupLabels[2].textContent.startsWith("European Ancestry"), `should be the expected group name`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort sample groups by Sample Count", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSampleGrpsBy: "sampleCount"
+            }
+          },
+          divideBy: {
+            id: "genetic_race"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const matrixGroupLabels = matrix.Inner.dom.sampleLabelsPG.selectAll(
+      ".sjpp-matrix-series-group-label-g .sjpp-matrix-label"
+    )._groups[0];
+    test.true(matrixGroupLabels[0].textContent.startsWith("European Ancestry"), `should be the expected group name`);
+    test.true(matrixGroupLabels[2].textContent.startsWith("Asian Ancestry"), `should be the expected group name`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort sample groups by Hits", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      nav: {
+        activeTab: 1
+      },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSampleGrpsBy: "hits"
+            }
+          },
+          divideBy: {
+            id: "Hearing loss"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const matrixGroupLabels = matrix.Inner.dom.sampleLabelsPG.selectAll(
+      ".sjpp-matrix-series-group-label-g .sjpp-matrix-label"
+    )._groups[0];
+    test.true(matrixGroupLabels[0].textContent.startsWith("3: Severe"), `should be the expected group name`);
+    test.true(matrixGroupLabels[4].textContent.startsWith("1: Mild"), `should be the expected group name`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sort sample groups by Hits 2", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          id: "xyz",
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortSampleGrpsBy: "hits"
+            }
+          },
+          divideBy: {
+            id: "agedx"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        postRender: runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender", null);
+    const matrixGroupLabels = matrix.Inner.dom.sampleLabelsPG.selectAll(
+      ".sjpp-matrix-series-group-label-g .sjpp-matrix-label"
+    )._groups[0];
+    test.true(matrixGroupLabels[0].textContent.startsWith("10 to <15"), `should have the expected left-most group name`);
+    test.true(matrixGroupLabels[4].textContent.startsWith("\u226520"), `should have the right-most expected group name`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Display Sample Counts for Gene: Absolute", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              samplecount4gene: "abs"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label")._groups[0];
+    const pattern = /\(\d+\)/;
+    test.true(pattern.test(termLabels[0].textContent), `should display sample counts for gene by absolute number`);
+    test.true(
+      pattern.test(termLabels[termLabels.length - 1].textContent),
+      `should display sample counts for gene by absolute number`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Display Sample Counts for Gene: Percent", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              samplecount4gene: "pct"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label")._groups[0];
+    const pattern = /\(\d+(\.\d+)? ?%\)/;
+    test.true(pattern.test(termLabels[0].textContent), `should display sample counts for gene by percentage`);
+    test.true(
+      pattern.test(termLabels[termLabels.length - 1].textContent),
+      `should display sample counts for gene by percentage`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Display Sample Counts for Gene: None", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              samplecount4gene: ""
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label")._groups[0];
+    const pattern = /\(\d+(\.\d+)?%\)|\(\d+\)/g;
+    test.true(!pattern.test(termLabels[0].textContent), `should not display sample counts for gene`);
+    test.true(!pattern.test(termLabels[termLabels.length - 1].textContent), `should not display sample counts for gene`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Sort Genes By Sample Count", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortTermsBy: "sampleCount"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label")._groups[0];
+    test.true(termLabels[0].textContent.startsWith("AKT1"), `should sort genes by sample count`);
+    test.true(termLabels[2].textContent.startsWith("KRAS"), `should sort genes by sample count`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Sort Genes By Input Data Order", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortTermsBy: "asListed"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label")._groups[0];
+    test.true(termLabels[0].textContent.startsWith("TP53"), `should sort genes by input data order`);
+    test.true(termLabels[2].textContent.startsWith("AKT1"), `should sort genes by input data order`);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("avoid race condition - plot edit", function(test) {
+  test.timeoutAfter(1500);
+  test.plan(4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortTermsBy: "asListed"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    matrix.Inner.app.vocabApi.origGetAnnotatedSampleData = matrix.Inner.app.vocabApi.getAnnotatedSampleData;
+    matrix.Inner.app.vocabApi.getAnnotatedSampleData = async (opts, _refs = {}) => {
+      const j = i;
+      i = 0;
+      const data = await matrix.Inner.app.vocabApi.origGetAnnotatedSampleData(opts, _refs);
+      await sleep(j);
+      return data;
+    };
+    matrix.on("postRender.test", async () => {
+      matrix.on("postRender.test", null);
+      await sleep(responseDelay + 300);
+      const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label");
+      test.equal(termLabels.size(), 1, `should have 1 gene row`);
+      test.true(termLabels._groups?.[0][0].textContent.startsWith("BCR"), `should sort genes by input data order`);
+      const rects = matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
+      const hits = rects.filter((d) => d.key === "BCR" && d.value.class != "WT" && d.value.class != "Blank");
+      test.equal(
+        rects.size(),
+        240,
+        "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
+      );
+      test.equal(hits.size(), 2, "should have the expected number of matrix cell rects with hits");
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    });
+    const responseDelay = 10;
+    let i = responseDelay;
+    try {
+      const results = await Promise.all([
+        matrix.Inner.app.dispatch({
+          type: "plot_edit",
+          id: matrix.id,
+          config: {
+            termgroups: [
+              {
+                name: "",
+                lst: [
+                  // $id is added manually since fillTermWrapper() is not called here and
+                  // cannot be assumed to be called within store.plot_edit()
+                  {
+                    $id: 0,
+                    term: {
+                      gene: "KRAS",
+                      name: "KRAS",
+                      type: "geneVariant",
+                      isleaf: true,
+                      groupsetting: { disabled: false }
+                    },
+                    q: { type: "values" }
+                  },
+                  {
+                    $id: 1,
+                    term: {
+                      gene: "AKT1",
+                      name: "AKT1",
+                      type: "geneVariant",
+                      isleaf: true,
+                      groupsetting: { disabled: false }
+                    },
+                    q: { type: "values" }
+                  }
+                ]
+              }
+            ]
+          }
+        }),
+        (async () => {
+          await sleep(1);
+          matrix.Inner.app.dispatch({
+            type: "plot_edit",
+            id: matrix.id,
+            config: {
+              termgroups: [
+                {
+                  name: "",
+                  // $id is added manually since fillTermWrapper() is not called here and
+                  // cannot be assumed to be called within store.plot_edit()
+                  lst: [
+                    {
+                      $id: 3,
+                      term: {
+                        name: "BCR",
+                        genes: [
+                          {
+                            kind: "gene",
+                            id: "BCR",
+                            gene: "BCR",
+                            name: "BCR",
+                            type: "geneVariant"
+                          }
+                        ],
+                        type: "geneVariant",
+                        isleaf: true,
+                        groupsetting: { disabled: false }
+                      },
+                      q: { type: "values" }
+                    }
+                  ]
+                }
+              ]
+            }
+          });
+        })()
+      ]);
+    } catch (e) {
+      test.fail("error: " + e);
+      throw e;
+    }
+  }
+});
+(0, import_tape.default)("avoid race condition - cohort change", function(test) {
+  test.timeoutAfter(3e3);
+  test.plan(4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200,
+              sortTermsBy: "asListed"
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: getGenes()
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    matrix.Inner.app.vocabApi.origGetAnnotatedSampleData = matrix.Inner.app.vocabApi.getAnnotatedSampleData;
+    matrix.Inner.app.vocabApi.getAnnotatedSampleData = async (opts, _refs = {}) => {
+      const vkeys = opts.filter.lst?.[0].tvs.values.map((v) => v.key);
+      const j = responseDelays[i];
+      i++;
+      await sleep(j);
+      const data = await matrix.Inner.app.vocabApi.origGetAnnotatedSampleData(opts, _refs);
+      return data;
+    };
+    matrix.on("postRender.test", async () => {
+      matrix.on("postRender.test", null);
+      await sleep(responseDelays.reduce((sum, v) => sum + v, 0) + 300);
+      const termLabels = matrix.Inner.dom.termLabelG.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label");
+      test.equal(termLabels.size(), 3, `should have 3 gene rows`);
+      const rects = matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
+      test.equal(
+        rects.size(),
+        1202,
+        "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
+      );
+      const hits = rects.filter((d) => d.key === "BCR" && d.value.class != "WT" && d.value.class != "Blank");
+      test.equal(hits.size(), 0, "should have the expected number of matrix cell rects with hits");
+      test.deepEqual(
+        matrix.Inner.app.getState().termfilter.filter.lst?.[0].tvs,
+        matrix.Inner.state.filter.lst?.[0].tvs,
+        `app.state and matrix.state should have the same cohort filter value`
+      );
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    });
+    const responseDelays = [800, 500, 10];
+    let i = 0;
+    try {
+      const results = await Promise.all([
+        (async () => {
+          await sleep(100);
+          matrix.Inner.app.dispatch({
+            type: "cohort_set",
+            activeCohort: 1
+          });
+        })(),
+        (async () => {
+          await sleep(200);
+          matrix.Inner.app.dispatch({
+            type: "cohort_set",
+            activeCohort: 0
+          });
+        })(),
+        (async () => {
+          await sleep(300);
+          matrix.Inner.app.dispatch({
+            type: "cohort_set",
+            activeCohort: 2
+          });
+        })()
+      ]);
+    } catch (e) {
+      test.fail("error: " + e);
+      throw e;
+    }
+  }
+});
+(0, import_tape.default)('apply "hide" legend filters to a dictionary term', function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(10);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "genetic_race"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                  // or 'continuous'
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Asian")
+    );
+    legendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(options[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(options[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(options[2].innerText, "Show all", `third option should be Show all`);
+    const rects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 177,
+      trigger: () => {
+        options[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const legendTexts2 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Asian")
+    );
+    legendTexts2.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options2 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(options2[0].innerText, "Show", `First option should be Show`);
+    test.equal(options2[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(options2[2].innerText, "Show all", `third option should be Show all`);
+    const rects2 = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 180,
+      trigger: () => {
+        options2[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('apply "show only" and "show all" legend filters to dictionary terms', function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(14);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "sex"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                  // or 'continuous'
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Male")
+    );
+    legendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    const rects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 75,
+      trigger: () => {
+        options[1].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const secondLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("<5")
+    );
+    secondLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const secondOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(secondOptions[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(secondOptions[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(secondOptions[2].innerText, "Show all", `third option should be Show all`);
+    const secondRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 30,
+      trigger: () => {
+        secondOptions[1].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const thirdLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("<5")
+    );
+    thirdLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const thirdOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(thirdOptions[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(thirdOptions[2].innerText, "Show all", `third option should be Show all`);
+    const thirdRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 0,
+      trigger: () => {
+        thirdOptions[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      0,
+      `should render the expected number of serieses`
+    );
+    const fourthLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("<5")
+    );
+    fourthLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const fourthOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(fourthOptions[0].innerText, "Show", `first option should be Show`);
+    test.equal(fourthOptions[2].innerText, "Show all", `third option should be Show all`);
+    const fourthRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 75,
+      trigger: () => {
+        fourthOptions[2].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)(
+  'apply "Hide samples with" and "Do not show" legend filters to a geneVariant term in geneVariant term only matrix',
+  function(test) {
+    test.timeoutAfter(5e3);
+    test.plan(12);
+    runpp({
+      state: {
+        plots: [
+          {
+            chartType: "matrix",
+            settings: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              matrix: {
+                availContentWidth: 1200
+              }
+            },
+            termgroups: [
+              {
+                name: "",
+                lst: [getGenes()[0]]
+              }
+            ]
+          }
+        ]
+      },
+      matrix: {
+        callbacks: {
+          "postRender.test": runTests
+        }
+      }
+    });
+    async function runTests(matrix) {
+      matrix.on("postRender.test", null);
+      const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Germline Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options[0].innerText,
+        "Hide samples with FRAMESHIFT",
+        `First option should be "Hide samples with FRAMESHIFT"`
+      );
+      test.equal(options[1].innerText, "Do not show FRAMESHIFT", `second option should be "Do not show FRAMESHIFT"`);
+      test.equal(options.length, 2, `Should only show two options`);
+      const rects = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 237,
+        trigger: () => {
+          options[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      test.equal(
+        matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+        1,
+        `should render the expected number of serieses`
+      );
+      test.equal(
+        matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+        1,
+        `should render the expected number of cluster rects`
+      );
+      const legendTexts2 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Germline Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts2.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options2 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options2[0].innerText,
+        "Show samples with FRAMESHIFT",
+        `First option should be "Show samples with FRAMESHIFT"`
+      );
+      test.equal(options2.length, 1, `Should only show one option`);
+      const rects2 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 242,
+        trigger: () => {
+          options2[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      test.equal(
+        matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+        1,
+        `should render the expected number of serieses`
+      );
+      test.equal(
+        matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+        1,
+        `should render the expected number of cluster rects`
+      );
+      const legendTexts3 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Germline Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts3.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options3 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(options3.length, 2, `Should only show two options`);
+      const rects3 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 241,
+        trigger: () => {
+          options3[1].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      const legendTexts4 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Germline Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts4.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options4 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options4[0].innerText,
+        "Show samples with FRAMESHIFT",
+        `First option should be "Show samples with FRAMESHIFT"`
+      );
+      test.equal(options4.length, 1, `Should only show one option`);
+      const rects4 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 242,
+        trigger: () => {
+          options4[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    }
+  }
+);
+(0, import_tape.default)("apply legend group filters to a geneVariant term in geneVariant term only matrix", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(15);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [{ term: { gene: "TP53", name: "TP53", type: "geneVariant", isleaf: true } }]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+    );
+    legendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(
+      options[0].innerText,
+      "Show only truncating mutations",
+      `First option should be "Show only truncating mutations"`
+    );
+    test.equal(
+      options[1].innerText,
+      "Show only protein-changing mutations",
+      `second option should be "Show only protein-changing mutations"`
+    );
+    test.equal(
+      options[2].innerText,
+      "Do not show Somatic Mutations",
+      `third option should be "Do not show Somatic Mutations"`
+    );
+    test.equal(options.length, 3, `Should show three options`);
+    const rects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 183,
+      trigger: () => {
+        options[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    const legendTexts2 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+    );
+    legendTexts2.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options2 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(
+      options2[2].innerText,
+      "Do not show Somatic Mutations",
+      `third option should be "Do not show Somatic Mutations"`
+    );
+    test.equal(
+      options2[3].innerText,
+      "Show all Somatic Mutations",
+      `fourth option should be "Show all Somatic Mutations"`
+    );
+    test.equal(options2.length, 4, `Should show four options`);
+    const rects2 = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 185,
+      trigger: () => {
+        options2[1].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    const legendTexts3 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+    );
+    legendTexts3.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options3 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(
+      options3[2].innerText,
+      "Do not show Somatic Mutations",
+      `third option should be "Do not show Somatic Mutations"`
+    );
+    test.equal(options3.length, 4, `Should show four options`);
+    const rects3 = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 182,
+      trigger: () => {
+        options3[2].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    const legendTexts4 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+    );
+    legendTexts4.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options4 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(
+      options4[0].innerText,
+      "Show all Somatic Mutations",
+      `first option should be "Show all Somatic Mutations"`
+    );
+    test.equal(options4.length, 1, `Should show one option`);
+    const rects4 = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 242,
+      trigger: () => {
+        options4[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)(
+  "apply legend group filters and legend filters to a matrix with both geneVariant and dictionary terms",
+  function(test) {
+    test.timeoutAfter(5e3);
+    test.plan(13);
+    runpp({
+      state: {
+        plots: [
+          {
+            chartType: "matrix",
+            settings: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              matrix: {
+                availContentWidth: 1200
+              }
+            },
+            termgroups: [
+              {
+                name: "",
+                lst: [
+                  ...getGenes(),
+                  { id: "agedx", term: termjson["agedx"] },
+                  { id: "diaggrp", term: termjson["diaggrp"] },
+                  { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+                ]
+              }
+            ]
+          }
+        ]
+      },
+      matrix: {
+        callbacks: {
+          "postRender.test": runTests
+        }
+      }
+    });
+    async function runTests(matrix) {
+      matrix.on("postRender.test", null);
+      const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+      );
+      legendTexts.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options[0].innerText,
+        "Show only truncating mutations",
+        `First option should be "Show only truncating mutations"`
+      );
+      test.equal(options.length, 3, `Should show three options`);
+      const rects = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 723,
+        trigger: () => {
+          options[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      test.equal(
+        matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+        6,
+        `should render the expected number of serieses`
+      );
+      const legendTexts2 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+      );
+      legendTexts2.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options2 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options2[1].innerText,
+        "Show only protein-changing mutations",
+        `second option should be "Show only protein-changing mutations"`
+      );
+      test.equal(
+        options2[3].innerText,
+        "Show all Somatic Mutations",
+        `fourth option should be "Show all Somatic Mutations"`
+      );
+      test.equal(options2.length, 4, `Should show four options`);
+      const rects2 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 726,
+        trigger: () => {
+          options2[1].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      const legendTexts3 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Somatic Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts3.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options3 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options3[0].innerText,
+        "Hide samples with FRAMESHIFT",
+        `First option should be "Hide samples with FRAMESHIFT"`
+      );
+      test.equal(options3[1].innerText, "Do not show FRAMESHIFT", `second option should be "Do not show FRAMESHIFT"`);
+      const rects3 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 712,
+        trigger: () => {
+          options3[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      test.equal(
+        matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+        6,
+        `should render the expected number of serieses`
+      );
+      const legendTexts4 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.$id?.startsWith("Somatic Mutations") && d.__data__.text?.startsWith("FRAMESHIFT")
+      );
+      legendTexts4.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options4 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options4[0].innerText,
+        "Show samples with FRAMESHIFT",
+        `First option should be "Show samples with FRAMESHIFT"`
+      );
+      test.equal(options4.length, 1, `Should only show one option`);
+      const rects4 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 726,
+        trigger: () => {
+          options4[0].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      const legendTexts5 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+        (d) => d?.__data__?.name == "Somatic Mutations" && !d.__data__.isLegendItem
+      );
+      legendTexts5.dispatchEvent(
+        new MouseEvent("mouseup", {
+          bubbles: true,
+          cancelable: true
+        })
+      );
+      const options5 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+      test.equal(
+        options5[3].innerText,
+        "Show all Somatic Mutations",
+        `fourth option should be "Show all Somatic Mutations"`
+      );
+      test.equal(options5.length, 4, `Should show four options`);
+      const rects5 = await detectLst({
+        elem: matrix.Inner.dom.seriesesG.node(),
+        selector: ".sjpp-mass-series-g rect",
+        count: 902,
+        trigger: () => {
+          options5[3].dispatchEvent(
+            new MouseEvent("click", {
+              bubbles: true,
+              cancelable: true
+            })
+          );
+        }
+      });
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    }
+  }
+);
+(0, import_tape.default)("cell brush zoom in", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(1);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 300
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "sex"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                  // or 'continuous'
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const startCell = matrix.Inner.serieses[1].cells[10];
+    const endCell = matrix.Inner.serieses[1].cells[14];
+    matrix.Inner.clickedSeriesCell = {
+      startCell,
+      endCell
+    };
+    matrix.Inner.zoomWidth = Math.abs(startCell.totalIndex - endCell.totalIndex) * matrix.Inner.dimensions.colw;
+    matrix.on("postRender.test", () => {
+      matrix.on("postRender.test", null);
+      test.deepEqual(matrix.Inner.settings.matrix.zoomLevel, 3.2, "should have the expected zoom level after zoom in");
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    });
+    matrix.Inner.triggerZoomArea();
+  }
+});
+(0, import_tape.default)("survival term in continous mode", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  term: {
+                    name: "Overall survival",
+                    type: "survival",
+                    isleaf: true,
+                    unit: "years",
+                    id: "os"
+                  },
+                  q: {
+                    mode: "continuous"
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      60,
+      `should render the expected number of cell rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term in discrete mode", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  term: {
+                    name: "Overall survival",
+                    type: "survival",
+                    isleaf: true,
+                    unit: "years",
+                    id: "os"
+                  },
+                  q: {
+                    mode: "continuous"
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      60,
+      `should render the expected number of cell rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term with divide by dictionary term", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "sex"
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  term: {
+                    name: "Overall survival",
+                    type: "survival",
+                    isleaf: true,
+                    unit: "years",
+                    id: "os"
+                  },
+                  q: {
+                    mode: "continuous"
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      1,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      60,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      2,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("dictionary term with divide by survival term", function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            // the matrix autocomputes the colw based on available screen width,
+            // need to set an exact screen width for consistent tests using getBBox()
+            matrix: {
+              availContentWidth: 1200
+            }
+          },
+          divideBy: {
+            id: "os"
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [
+                { id: "agedx", term: termjson["agedx"] },
+                { id: "diaggrp", term: termjson["diaggrp"] },
+                { id: "aaclassic_5", term: termjson["aaclassic_5"] }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      3,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g rect").size(),
+      180,
+      `should render the expected number of cell rects`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      2,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('apply "hide" and "show" legend filters to a survival term', function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(10);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "genetic_race"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                },
+                {
+                  term: {
+                    name: "Overall survival",
+                    type: "survival",
+                    isleaf: true,
+                    unit: "years",
+                    id: "os"
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Alive")
+    );
+    legendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(options[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(options[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(options[2].innerText, "Show all", `third option should be Show all`);
+    const rects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 228,
+      trigger: () => {
+        options[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const legendTexts2 = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Alive")
+    );
+    legendTexts2.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options2 = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(options2[0].innerText, "Show", `First option should be Show`);
+    test.equal(options2[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(options2[2].innerText, "Show all", `third option should be Show all`);
+    const rects2 = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 240,
+      trigger: () => {
+        options2[0].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('apply "show only" and "show all" legend filters to a survival terms', function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(14);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          termgroups: [
+            {
+              name: "",
+              lst: [
+                {
+                  id: "aaclassic_5",
+                  q: {
+                    mode: "continuous"
+                  }
+                },
+                {
+                  id: "genetic_race"
+                  //q: { mode: 'values' } // or 'groupsetting'
+                },
+                {
+                  id: "agedx",
+                  q: {
+                    mode: "discrete",
+                    type: "regular-bin",
+                    bin_size: 5,
+                    first_bin: {
+                      startunbounded: true,
+                      stop: 5,
+                      stopinclusive: true
+                    }
+                  }
+                },
+                {
+                  term: {
+                    name: "Overall survival",
+                    type: "survival",
+                    isleaf: true,
+                    unit: "years",
+                    id: "os"
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const legendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Alive")
+    );
+    legendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const options = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    const rects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 12,
+      trigger: () => {
+        options[1].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const secondLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("<5")
+    );
+    secondLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const secondOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(secondOptions[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(secondOptions[1].innerText, "Show only", `second option should be Show only`);
+    test.equal(secondOptions[2].innerText, "Show all", `third option should be Show all`);
+    const secondRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 4,
+      trigger: () => {
+        secondOptions[1].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    const thirdLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("<5")
+    );
+    thirdLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const thirdOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(thirdOptions[0].innerText, "Hide", `First option should be Hide`);
+    test.equal(thirdOptions[2].innerText, "Show all", `third option should be Show all`);
+    const thirdRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 12,
+      trigger: () => {
+        thirdOptions[2].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    const fourthLegendTexts = [...matrix.Inner.dom.legendG.node().querySelectorAll("g g text")].find(
+      (d) => d?.__data__?.text?.startsWith("Alive")
+    );
+    fourthLegendTexts.dispatchEvent(
+      new MouseEvent("mouseup", {
+        bubbles: true,
+        cancelable: true
+      })
+    );
+    const fourthOptions = matrix.Inner.dom.legendMenu.d.node().querySelectorAll("div.sja_menuoption.sja_sharp_border");
+    test.equal(fourthOptions[0].innerText, "Hide", `first option should be Hide`);
+    test.equal(fourthOptions[2].innerText, "Show all", `third option should be Show all`);
+    const fourthRects = await detectLst({
+      elem: matrix.Inner.dom.seriesesG.node(),
+      selector: ".sjpp-mass-series-g rect",
+      count: 240,
+      trigger: () => {
+        fourthOptions[2].dispatchEvent(
+          new MouseEvent("click", {
+            bubbles: true,
+            cancelable: true
+          })
+        );
+      }
+    });
+    test.equal(
+      matrix.Inner.dom.seriesesG.selectAll(".sjpp-mass-series-g").size(),
+      4,
+      `should render the expected number of serieses`
+    );
+    test.equal(
+      matrix.Inner.dom.cluster.selectAll(".sjpp-matrix-clusteroutlines rect").size(),
+      1,
+      `should render the expected number of cluster rects`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("sample ancestry labels and line spans", function(test) {
+  test.timeoutAfter(8e3);
+  const ancestrySampleIds = [1, 2, 3, 4, 5, 6, 7, 8, 9];
+  const filter = {
+    type: "tvslst",
+    in: true,
+    join: "",
+    lst: [
+      {
+        type: "tvs",
+        noEdit: true,
+        tvs: {
+          term: {
+            name: "ancestry test samples",
+            type: "samplelst",
+            values: { grp: { key: "grp", list: ancestrySampleIds.map((id) => ({ sampleId: id })) } }
+          }
+        }
+      }
+    ]
+  };
+  runpp({
+    state: {
+      // samples 1-9 belong to the XYZ cohort (index 1); the store ANDs the active
+      // cohort filter with the samplelst filter below to yield exactly samples 1-9
+      activeCohort: 1,
+      termfilter: { filter },
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            matrix: {
+              availContentWidth: 1200,
+              sortBySampleAncestry: "last"
+            }
+          },
+          termgroups: [
+            {
+              name: "Demographics",
+              lst: [{ id: "diaggrp" }]
+            }
+          ]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    test.equal(matrix.Inner.sampleOrder.length, 9, "should render the 9 filtered samples");
+    const spanNodes = matrix.Inner.dom.svg.selectAll(".sjpp-matrix-label-span").nodes();
+    test.equal(spanNodes.length, 3, "should render 3 ancestor spans (1_patient, 2_patient, and the nested 3_patient)");
+    const lineX2ByLabel = {};
+    for (const node of spanNodes) {
+      const label = node.querySelector("text")?.textContent;
+      lineX2ByLabel[label] = +node.querySelector("line")?.getAttribute("x2");
+    }
+    test.deepEqual(
+      Object.keys(lineX2ByLabel).sort(),
+      ["1_patient", "2_patient", "3_patient"],
+      "ancestor spans should be labeled by ancestor name (1_patient, 2_patient, 3_patient)"
+    );
+    test.equal(
+      matrix.Inner.dom.svg.selectAll(".sjpp-matrix-label-span line").size(),
+      3,
+      "should render 3 ancestor line spans"
+    );
+    test.ok(
+      lineX2ByLabel["3_patient"] > lineX2ByLabel["1_patient"] && lineX2ByLabel["3_patient"] > lineX2ByLabel["2_patient"],
+      "the nested grandparent span (3_patient) should be wider than the parent spans (1_patient, 2_patient)"
+    );
+    matrix.on("postRender.disableTest", () => {
+      matrix.on("postRender.disableTest", null);
+      test.equal(
+        matrix.Inner.dom.svg.selectAll(".sjpp-matrix-label-span").size(),
+        0,
+        "ancestor spans should be removed after sortBySampleAncestry is disabled"
+      );
+      if (test._ok) matrix.Inner.app.destroy();
+      test.end();
+    });
+    matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: { settings: { matrix: { sortBySampleAncestry: false } } }
+    });
+  }
+});
+var runpp = getRunPp("mass", {
+  state: {
+    dslabel: "TermdbTest",
+    genome: "hg38-test",
+    nav: { activeTab: -1 }
+  },
+  debug: 1
+});
+function getGenes() {
+  return [
+    { term: { gene: "TP53", name: "TP53", type: "geneVariant", isleaf: true } },
+    { term: { gene: "KRAS", name: "KRAS", type: "geneVariant", isleaf: true } },
+    { term: { gene: "AKT1", name: "AKT1", type: "geneVariant", isleaf: true } }
+  ];
+}
+function getTermCollection() {
+  return {
+    //isAtomic: true,
+    type: "TermCollectionTWCont",
+    //$id: 'TwBase_0__48243_99155',
+    term: {
+      type: "termCollection",
+      termlst: [
+        {
+          type: "float",
+          bins: {
+            default: {
+              type: "regular-bin",
+              bin_size: 5,
+              startinclusive: true,
+              first_bin: { startunbounded: true, stop: 5 }
+            },
+            label_offset: 1
+          },
+          name: "Age (years) at Cancer Diagnosis",
+          id: "agedx",
+          isleaf: true,
+          values: {},
+          hashtmldetail: true
+        },
+        {
+          type: "float",
+          bins: {
+            default: {
+              type: "regular-bin",
+              startinclusive: true,
+              bin_size: 5,
+              first_bin: { stop: 25 },
+              last_bin: { start: 55 }
+            }
+          },
+          name: "Age (years) at Death",
+          id: "a_death",
+          isleaf: true,
+          values: {},
+          hashtmldetail: true
+        },
+        {
+          type: "float",
+          bins: { default: { type: "regular-bin", startinclusive: true, bin_size: 10, first_bin: { stop: 15 } } },
+          name: "Age (years) at Last NDI Search",
+          id: "a_ndi",
+          isleaf: true,
+          values: {}
+        },
+        {
+          type: "float",
+          bins: { default: { type: "regular-bin", startinclusive: true, bin_size: 10, first_bin: { stop: 15 } } },
+          values: { "-994": { label: "N/A: No campus visit", uncomputable: true } },
+          name: "Age at last ABC assessment",
+          id: "agelastvisit",
+          isleaf: true
+        }
+      ],
+      name: "Fake Collection 1",
+      isleaf: true,
+      propsByTermId: {
+        agedx: { color: "#1b9e77" },
+        a_death: { color: "#d95f02" },
+        a_ndi: { color: "#7570b3" },
+        agelastvisit: { color: "#e7298a" }
+      }
+    },
+    q: { isAtomic: true, mode: "continuous", lst: [] }
+  };
+}
+//# sourceMappingURL=matrix.integration.spec-2N237E7T.js.map