@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/regression.spec-HEXCL3QV.js

@@ -0,0 +1,708 @@
+import {
+  getRunPp
+} from "./chunk-H34LAFGH.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import "./chunk-FDPWWODM.js";
+import "./chunk-UQ5CDHYF.js";
+import "./chunk-TTC4MNEM.js";
+import "./chunk-D5CVYITI.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-E76O5Z42.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-WKNI3HRQ.js";
+import "./chunk-A4Z3CI24.js";
+import "./chunk-PSJVMAWA.js";
+import "./chunk-KUZPTJJO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-C4BCMAIK.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-Z457XQSX.js";
+import "./chunk-AI2LUQS6.js";
+import "./chunk-2JR7RPB6.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-TLTS33EY.js";
+import "./chunk-2U2CP2Y2.js";
+import "./chunk-ZF6HNVYD.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/test/regression.spec.js
+var import_tape = __toESM(require_tape(), 1);
+var raceGroupsetting = {
+  id: "genetic_race",
+  q: {
+    type: "custom-groupset",
+    customset: {
+      groups: [
+        {
+          name: "group 123",
+          type: "values",
+          values: [{ key: "European Ancestry" }, { key: "Multi-Ancestry-Admixed" }]
+        },
+        { name: "group 456", type: "values", values: [{ key: "African Ancestry" }, { key: "Asian Ancestry" }] }
+      ]
+    }
+  }
+};
+var diaggrpGroupsetting = {
+  id: "diaggrp",
+  q: {
+    type: "custom-groupset",
+    customset: {
+      groups: [
+        {
+          name: "Leukemia",
+          type: "values",
+          values: [
+            { key: "Acute lymphoblastic leukemia" },
+            { key: "Chronic myeloid leukemia" },
+            { key: "Other leukemia" },
+            { key: "Acute myeloid leukemia" }
+          ]
+        },
+        {
+          name: "Lymphoma",
+          type: "values",
+          values: [{ key: "Hodgkin lymphoma" }, { key: "Non-Hodgkin lymphoma" }]
+        },
+        {
+          name: "Solid",
+          type: "values",
+          values: [{ key: "Central nervous system (CNS)" }, { key: "Neuroblastoma" }]
+        }
+      ]
+    }
+  }
+};
+var pgsRegularBin = {
+  id: "prs_PGS000332",
+  q: {
+    type: "regular-bin",
+    startinclusive: true,
+    bin_size: 0.4,
+    first_bin: {
+      stop: -1,
+      startunbounded: true
+    },
+    rounding: ".1f"
+  },
+  refGrp: "-0.2 to <0.2"
+};
+var pgsCustomBin = {
+  id: "prs_PGS000332",
+  q: {
+    type: "custom-bin",
+    lst: [
+      {
+        startunbounded: true,
+        stop: -0.5,
+        stopinclusive: false,
+        label: "<0.5"
+      },
+      {
+        start: -0.5,
+        stop: 0,
+        stopinclusive: false,
+        label: "-0.5 to 0"
+      },
+      {
+        start: 0,
+        startinclusive: true,
+        stopunbounded: true,
+        label: "\u22650"
+      }
+    ]
+  }
+};
+var agedxCustomBin = {
+  id: "agedx",
+  q: {
+    type: "custom-bin",
+    lst: [
+      {
+        startunbounded: true,
+        stop: 1,
+        stopinclusive: false,
+        label: "Infants: <1"
+      },
+      {
+        start: 1,
+        stop: 4,
+        stopinclusive: false,
+        label: "Toddlers: 1-4"
+      },
+      {
+        start: 4,
+        startinclusive: true,
+        stopunbounded: true,
+        label: "\u22654"
+      }
+    ]
+  }
+};
+var snplst = {
+  term: {
+    type: "snplst",
+    id: "snplstTermId",
+    snps: [
+      { rsid: "rs1641548", effectAllele: "T" },
+      { rsid: "rs858528", effectAllele: "T" },
+      { rsid: "rs1642793", effectAllele: "C" },
+      { rsid: "rs1042522" },
+      { rsid: "rs1642782" },
+      { rsid: "rs6503048" }
+    ]
+  },
+  q: {
+    AFcutoff: 5,
+    alleleType: 0,
+    geneticModel: 0,
+    missingGenotype: 0,
+    restrictAncestry: {
+      name: "European ancestry",
+      tvs: {
+        term: {
+          id: "genetic_race",
+          type: "categorical",
+          name: "Genetically defined race"
+        },
+        values: [{ key: "European Ancestry", label: "European Ancestry" }]
+      }
+    }
+  }
+};
+var snplocus = {
+  term: {
+    type: "snplocus",
+    id: "snplocusTermId"
+  },
+  q: {
+    chr: "chr17",
+    start: 7674304,
+    stop: 7676849,
+    AFcutoff: 5,
+    alleleType: 0,
+    geneticModel: 0,
+    restrictAncestry: {
+      name: "European ancestry",
+      tvs: {
+        term: {
+          id: "genetic_race",
+          type: "categorical",
+          name: "Genetically defined race"
+        },
+        values: [{ key: "European Ancestry", label: "European Ancestry" }]
+      }
+    },
+    variant_filter: {
+      type: "tvslst",
+      join: "and",
+      in: true,
+      lst: [
+        /*
+        {
+        	type: 'tvs',
+        	tvs: {
+        		isnot: true,
+        		values: [{ label: 'Bad', key: 'Bad' }],
+        		term: {
+        			id: 'QC_sjlife',
+        			name: 'ABC classification',
+        			parent_id: null,
+        			isleaf: true,
+        			type: 'categorical',
+        			values: {
+        				SuperGood: { label: 'SuperGood', key: 'SuperGood' },
+        				Good: { label: 'Good', key: 'Good' },
+        				Ambiguous: { label: 'Ambiguous', key: 'Ambiguous' },
+        				Bad: { label: 'Bad', key: 'Bad' }
+        			}
+        		}
+        	}
+        },
+        */
+        /*
+        {
+        	type: 'tvs',
+        	tvs: {
+        		isnot: true,
+        		values: [{ label: 'Bad', key: 'Bad' }],
+        		term: {
+        			id: 'QC_ccss',
+        			name: 'XYZ classification',
+        			parent_id: null,
+        			isleaf: true,
+        			type: 'categorical',
+        			values: {
+        				SuperGood: { label: 'SuperGood', key: 'SuperGood' },
+        				Good: { label: 'Good', key: 'Good' },
+        				Ambiguous: { label: 'Ambiguous', key: 'Ambiguous' },
+        				Bad: { label: 'Bad', key: 'Bad' }
+        			}
+        		}
+        	}
+        },
+        */
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
+            term: { id: "SJcontrol_CR", name: "ABC control call rate", parent_id: null, isleaf: true, type: "float" }
+          }
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
+            term: { id: "CR", name: "Call rate, ABC+XYZ", parent_id: null, isleaf: true, type: "float" }
+          }
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
+            term: { id: "CR_sjlife", name: "ABC call rate", parent_id: null, isleaf: true, type: "float" }
+          }
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
+            term: { id: "CR_ccss", name: "XYZ call rate", parent_id: null, isleaf: true, type: "float" }
+          }
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
+            term: { id: "gnomAD_CR", name: "gnmoAD call rate", parent_id: null, isleaf: true, type: "float" }
+          }
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [{ start: 0.1, startinclusive: true, stopunbounded: true }],
+            term: {
+              id: "gnomAD_AF",
+              name: "gnomAD allele frequency",
+              parent_id: null,
+              isleaf: true,
+              type: "float",
+              min: 0,
+              max: 1,
+              values: {}
+            }
+          }
+        },
+        /*
+        {
+        	type: 'tvs',
+        	tvs: {
+        		isnot: true,
+        		values: [{ label: 'yes', key: '1' }],
+        		term: { id: 'BadBLAT', name: 'Paralog', parent_id: null, isleaf: true, type: 'categorical' }
+        	}
+        },
+        */
+        {
+          type: "tvs",
+          tvs: {
+            isnot: true,
+            values: [{ label: "yes", key: "1" }],
+            term: { id: "Polymer_region", name: "Polymer region", parent_id: null, isleaf: true, type: "categorical" }
+          }
+        }
+      ]
+    }
+  }
+};
+var testList = [
+  {
+    name: "sex race hrtavg",
+    // hrtavg is continuous
+    headingCount: 5,
+    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, { id: "hrtavg" }]
+  },
+  {
+    name: "sex*race hrtavg",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1", interactions: ["genetic_race"] },
+      { id: "genetic_race", interactions: ["sex"] },
+      { id: "hrtavg" }
+    ]
+  },
+  {
+    name: "sex race*hrtavg",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "genetic_race", interactions: ["hrtavg"] },
+      { id: "hrtavg", interactions: ["genetic_race"] }
+    ]
+  },
+  {
+    name: "sex hrtavg*agedx",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "hrtavg", interactions: ["agedx"] },
+      { id: "agedx", interactions: ["hrtavg"] }
+    ]
+  },
+  {
+    name: "sex raceGroupsetting hrtavg",
+    // groupsetting, continuous
+    headingCount: 5,
+    independent: [{ id: "sex", refGrp: "1" }, raceGroupsetting, { id: "hrtavg" }]
+  },
+  {
+    name: "sex*raceGroupsetting hrtavg",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1", interactions: ["genetic_race"] },
+      addInteraction(raceGroupsetting, "sex"),
+      { id: "hrtavg" }
+    ]
+  },
+  {
+    name: "sex raceGroupsetting*hrtavg",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(raceGroupsetting, "hrtavg"),
+      { id: "hrtavg", interactions: ["genetic_race"] }
+    ]
+  },
+  {
+    name: "raceGroupsetting*diaggrpGroupsetting",
+    headingCount: 5,
+    independent: [addInteraction(raceGroupsetting, "diaggrp"), addInteraction(diaggrpGroupsetting, "genetic_race")]
+  },
+  {
+    name: "sex race pgsRegularBin",
+    headingCount: 5,
+    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, pgsRegularBin]
+  },
+  {
+    name: "sex race*pgsRegularBin",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "genetic_race", interactions: ["prs_PGS000332"] },
+      addInteraction(pgsRegularBin, "genetic_race")
+    ]
+  },
+  {
+    name: "sex race pgsCustomBin",
+    headingCount: 5,
+    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, pgsCustomBin]
+  },
+  {
+    name: "sex race*pgsCustomBin",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "genetic_race", interactions: ["prs_PGS000332"] },
+      addInteraction(pgsCustomBin, "genetic_race")
+    ]
+  },
+  {
+    name: "pgsRegularBin*agedxCustomBin",
+    headingCount: 5,
+    independent: [addInteraction(pgsRegularBin, "agedx"), addInteraction(agedxCustomBin, "prs_PGS000332")]
+  },
+  {
+    name: "raceGroupsetting*pgsRegularBin",
+    headingCount: 5,
+    independent: [addInteraction(raceGroupsetting, "prs_PGS000332"), addInteraction(pgsRegularBin, "genetic_race")]
+  },
+  {
+    name: "raceGroupsetting*pgsCustomBin",
+    headingCount: 5,
+    independent: [addInteraction(pgsCustomBin, "genetic_race"), addInteraction(raceGroupsetting, "prs_PGS000332")]
+  },
+  {
+    name: "sex hrtavgSpline",
+    headingCount: 6,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
+    ]
+  },
+  {
+    name: "sex hrtavgSpline ageSpline",
+    headingCount: 6,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } },
+      { id: "agedx", q: { mode: "spline", knots: [{ value: 0.5 }, { value: 3.5 }, { value: 10.5 }] } }
+    ]
+  },
+  {
+    name: "sex diaggrp agedx hrtavgSpline snplst",
+    headingCount: 6,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "diaggrp" },
+      { id: "agedx" },
+      snplst,
+      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
+    ]
+  },
+  {
+    // cannot use diaggrp to interact with snplst, it will timeout
+    name: "sex income*snplst",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "homeinc", interactions: ["snplstTermId"] },
+      addInteraction(snplst, "homeinc")
+    ]
+  },
+  {
+    name: "sex hrtavg*snplst",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "hrtavg", interactions: ["snplstTermId"] },
+      addInteraction(snplst, "hrtavg")
+    ]
+  },
+  {
+    name: "sex pgsRegularBin*snplst",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(pgsRegularBin, "snplstTermId"),
+      addInteraction(snplst, "prs_PGS000332")
+    ]
+  },
+  {
+    name: "sex pgsCustomBin*snplst",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(pgsCustomBin, "snplstTermId"),
+      addInteraction(snplst, "prs_PGS000332")
+    ]
+  },
+  {
+    name: "sex diaggrpGroupsetting*snplst",
+    headingCount: 5,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(diaggrpGroupsetting, "snplstTermId"),
+      addInteraction(snplst, "diaggrp")
+    ]
+  },
+  {
+    name: "sex diaggrp agedx hrtavgSpline snplocus",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "diaggrp" },
+      { id: "agedx" },
+      snplocus,
+      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
+    ]
+  },
+  {
+    name: "sex income*snplocus",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "homeinc", interactions: ["snplocusTermId"] },
+      addInteraction(snplocus, "homeinc")
+    ]
+  },
+  {
+    name: "sex hrtavg*snplocus",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      { id: "hrtavg", interactions: ["snplocusTermId"] },
+      addInteraction(snplocus, "hrtavg")
+    ]
+  },
+  {
+    name: "sex pgsRegularBin*snplst",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(pgsRegularBin, "snplocusTermId"),
+      addInteraction(snplocus, "prs_PGS000332")
+    ]
+  },
+  {
+    name: "sex pgsCustomBin*snplocus",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(pgsCustomBin, "snplocusTermId"),
+      addInteraction(snplocus, "prs_PGS000332")
+    ]
+  },
+  {
+    name: "sex diaggrpGroupsetting*snplocus",
+    headingCount: 0,
+    independent: [
+      { id: "sex", refGrp: "1" },
+      addInteraction(diaggrpGroupsetting, "snplocusTermId"),
+      addInteraction(snplocus, "diaggrp")
+    ]
+  }
+];
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- mass/regression -***-");
+  test.end();
+});
+var activeTests = testList.filter((t) => t.runthis);
+for (const item of activeTests.length ? activeTests : testList) {
+  (0, import_tape.default)("(LINEAR) EF ~ " + item.name, (test) => {
+    test.timeoutAfter(5e4);
+    runpp(
+      {
+        regressionType: "linear",
+        outcome: { id: "LV_Ejection_Fraction_3D" },
+        independent: item.independent
+      },
+      async (reg) => {
+        reg.on("postRender.test", null);
+        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
+        mayDestroyDom(test, reg);
+        test.end();
+      },
+      test
+    );
+  });
+  (0, import_tape.default)("(LOGISTIC) EF ~ " + item.name, (test) => {
+    test.timeoutAfter(5e4);
+    runpp(
+      {
+        regressionType: "logistic",
+        outcome: { id: "LV_Ejection_Fraction_3D" },
+        independent: item.independent
+      },
+      async (reg) => {
+        reg.on("postRender.test", null);
+        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
+        mayDestroyDom(test, reg);
+        test.end();
+      },
+      test
+    );
+  });
+  (0, import_tape.default)("(LOGISTIC) Arrhythmias ~ " + item.name, (test) => {
+    test.timeoutAfter(5e4);
+    runpp(
+      {
+        regressionType: "logistic",
+        outcome: { id: "Arrhythmias" },
+        independent: item.independent
+      },
+      async (reg) => {
+        reg.on("postRender.test", null);
+        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
+        mayDestroyDom(test, reg);
+        test.end();
+      },
+      test
+    );
+  });
+  (0, import_tape.default)("(COX) Arrhythmias ~ " + item.name, (test) => {
+    test.timeoutAfter(5e4);
+    runpp(
+      {
+        regressionType: "cox",
+        outcome: { id: "Arrhythmias" },
+        independent: item.independent
+      },
+      async (reg) => {
+        reg.on("postRender.test", null);
+        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
+        mayDestroyDom(test, reg);
+        test.end();
+      },
+      test
+    );
+  });
+}
+function runpp(plot, runtest, test) {
+  plot.chartType = "regression";
+  getRunPp("mass", {
+    nav: {
+      activeTab: 1
+    },
+    state: {
+      genome: "hg38",
+      dslabel: "SJLife"
+    },
+    debug: 1
+  })({
+    state: { plots: [plot] },
+    app: {
+      callbacks: {
+        "postInit.test": (app, error = null) => {
+          if (!error) return;
+          test.fail("app.init() error: " + JSON.stringify(error));
+          test.end();
+        }
+      }
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runtest
+      }
+    }
+  });
+}
+function findResultHeadings(reg) {
+  if (reg.Inner.results.dom.err_div.style("display") == "block") {
+    return -1;
+  }
+  const spans = reg.Inner.results.dom.oneSetResultDiv.selectAll("span").nodes();
+  let foundNumber = 0;
+  foundNumber += spans.find((i) => i.innerText == "Sample size:") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Residuals") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Deviance residuals") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Cubic spline plots") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Coefficients") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Type III statistics") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Statistical tests") ? 1 : 0;
+  foundNumber += spans.find((i) => i.innerText == "Other summary statistics") ? 1 : 0;
+  return foundNumber;
+}
+function addInteraction(tw, interId) {
+  const a = JSON.parse(JSON.stringify(tw));
+  a.interactions = [interId];
+  return a;
+}
+function mayDestroyDom(test, component) {
+  if (!test._ok) return;
+  if (component.Inner.app) component.Inner.app.destroy();
+  else component.destroy();
+}
+//# sourceMappingURL=regression.spec-HEXCL3QV.js.map