@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-KZILNGAV.js

@@ -0,0 +1,187 @@
+import {
+  DATermTypes
+} from "./chunk-TKW5TW4Z.js";
+import {
+  dofetch3
+} from "./chunk-JVPWIVDT.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+
+// plots/volcano/colors.ts
+function getGroupColors(config) {
+  const groups = config?.samplelst?.groups;
+  const termValues = config?.tw?.term?.values;
+  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
+  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
+  return {
+    controlColor: toHex(rawDown, "red"),
+    caseColor: toHex(rawUp, "blue")
+  };
+}
+function toHex(color, fallback) {
+  const c = rgb(color || fallback);
+  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
+}
+
+// plots/volcano/model/VolcanoModel.ts
+var VolcanoModel = class {
+  /** TODO: This model is used in both the volcano and gsea.
+   * In the future, create base model in DA and use specific
+   * classes for the volcano and gsea. */
+  constructor(plot, termType) {
+    this.plot = plot;
+    this.app = plot.app;
+    this.termType = termType;
+  }
+  /** May use mapper instead as more termTypes are added */
+  async getData(config, settings) {
+    this.config = config;
+    this.settings = settings;
+    if (this.termType === DATermTypes.GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.PROTEOME_DAP) {
+      const body = this.getDapRequestBody();
+      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
+    }
+    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
+  }
+  //Gene expression
+  async getGERequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DE",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      method: this.settings.method,
+      min_count: this.settings.minCount,
+      min_total_count: this.settings.minTotalCount,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      cpm_cutoff: this.settings.cpmCutoff,
+      volcanoRender: this.getVolcanoRender()
+    };
+    const pseudobulk = this.config.tw?.pseudobulk;
+    if (pseudobulk) body.pseudobulk = pseudobulk;
+    this.addConfounderTw(body);
+    return body;
+  }
+  //DNA methylation
+  async getDMRequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DM",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      min_samples_per_group: this.settings.minSamplesPerGroup,
+      volcanoRender: this.getVolcanoRender()
+    };
+    this.addConfounderTw(body);
+    return body;
+  }
+  /** Parameters telling the server to run the `volcano` Rust renderer and return a
+   * volcano PNG + top-significant rows instead of the full dot list. */
+  getVolcanoRender() {
+    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
+    const { caseColor, controlColor } = getGroupColors(this.config);
+    return {
+      significanceThresholds: {
+        pValueCutoff: this.settings.pValue,
+        pValueType: this.settings.pValueType,
+        foldChangeCutoff: this.settings.foldChangeCutoff
+      },
+      pixelWidth: this.settings.width,
+      pixelHeight: this.settings.height,
+      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
+      colorSignificantUp: caseColor,
+      colorSignificantDown: controlColor,
+      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
+      dotRadius,
+      maxInteractiveDots: this.settings.maxInteractiveDots,
+      // Render the PNG at device-pixel resolution so it stays sharp on
+      // retina screens. The server reports the plot extent in CSS-space,
+      // so SVG overlay coords are unaffected.
+      //
+      // Oversample by 2× so the PNG also stays sharp when the user
+      // *zooms in after* the initial render (the captured DPR is frozen
+      // at fetch time — bigger headroom = more tolerable post-render
+      // zoom before pixelation appears). The server clamp keeps the
+      // bitmap memory bounded.
+      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
+    };
+  }
+  //This is a workaround until the server can accept an arr of confounder tws
+  addConfounderTw(body) {
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+  }
+  //Single cell cell type
+  getSCCTRequestBody() {
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      sample: this.config.sample,
+      termId: this.config.termId,
+      categoryName: this.config.categoryName,
+      volcanoRender: this.getVolcanoRender()
+    };
+    return body;
+  }
+  getDapRequestBody() {
+    const { organism, assay, cohort } = this.config.proteomeDetails;
+    return {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      organism,
+      assay,
+      cohort,
+      volcanoRender: this.getVolcanoRender()
+    };
+  }
+  /** retrieve the sampleId/sampleName for samples in
+   * the "others" group instead of using {in: false} */
+  async getOtherSamples(samplelst) {
+    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
+    if (!othersSamplesGroup) return;
+    const state = this.app.getState();
+    const samplesGroup = samplelst.groups.find((g) => g.in);
+    othersSamplesGroup.values = [];
+    for (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
+      if (samplesGroup.values.indexOf((i) => i.sampleId == s.id) == -1) {
+        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
+      }
+    }
+    othersSamplesGroup.in = true;
+  }
+};
+
+export {
+  getGroupColors,
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-KZILNGAV.js.map

package/dist/chunk-KZILNGAV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/volcano/colors.ts", "../plots/volcano/model/VolcanoModel.ts"],
+  "sourcesContent": ["import { rgb } from 'd3-color'\n\n/** Resolve the case/control dot colors for a volcano plot in one place so the\n * interactive SVG overlay (VolcanoViewModel) and the server-rendered PNG\n * (VolcanoModel \u2192 Rust) paint each dot the same color.\n *\n * `caseColor` maps to points with `fold_change > 0` (group 2 in samplelst),\n * `controlColor` to `fold_change < 0` (group 1). Every returned color is a\n * `#rrggbb` hex string \u2014 CSS names like `'red'` are normalized via d3-color\n * so the Rust renderer's hex-only parser doesn't fall back to a muted tuple.\n */\nexport function getGroupColors(config: any): { caseColor: string; controlColor: string } {\n\tconst groups = config?.samplelst?.groups\n\tconst termValues = config?.tw?.term?.values\n\tconst rawDown = termValues?.[groups?.[0]?.name]?.color || 'red'\n\tconst rawUp = termValues?.[groups?.[1]?.name]?.color || 'blue'\n\treturn {\n\t\tcontrolColor: toHex(rawDown, 'red'),\n\t\tcaseColor: toHex(rawUp, 'blue')\n\t}\n}\n\n/** Normalize any CSS-accepted color string into `#rrggbb`. */\nexport function toHex(color: string | undefined, fallback: string): string {\n\tconst c = rgb(color || fallback)\n\treturn c.displayable() ? c.formatHex() : rgb(fallback).formatHex()\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest, VolcanoRenderRequest } from '#types'\nimport { DATermTypes as tt } from '../../diffAnalysis/enabledTermTypes'\nimport { getGroupColors, toHex } from '../colors'\n// import type { Volcano } from '../Volcano'\n\nexport class VolcanoModel {\n\tplot: any\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\t/** TODO: This model is used in both the volcano and gsea.\n\t * In the future, create base model in DA and use specific\n\t * classes for the volcano and gsea. */\n\tconstructor(plot: any, termType: string) {\n\t\tthis.plot = plot\n\t\tthis.app = plot.app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === tt.GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\tconst response = await dofetch3('termdb/DE', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DE request so downstream plots (GSEA) can snapshot\n\t\t\t// it and later ask the server to recompute the DA cache if the\n\t\t\t// file is missing on a peer node or after TTL eviction.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffMeth', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DM request the same way the GE branch above does so\n\t\t\t// the GSEA tab can snapshot it and the server can recompute the DM\n\t\t\t// cache if the file is missing on a peer node or after TTL.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.PROTEOME_DAP) {\n\t\t\tconst body = this.getDapRequestBody()\n\t\t\treturn await dofetch3('termdb/dapVolcano', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_GENE_EXPRESSION) {\n\t\t\t//TODO\n\t\t}\n\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DE',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\t\tconst pseudobulk = this.config.tw?.pseudobulk\n\t\tif (pseudobulk) body.pseudobulk = pseudobulk\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DM',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffMethRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t/** Parameters telling the server to run the `volcano` Rust renderer and return a\n\t * volcano PNG + top-significant rows instead of the full dot list. */\n\tgetVolcanoRender(): VolcanoRenderRequest {\n\t\t// Match the client overlay's radius (see VolcanoViewModel.setPointData)\n\t\t// so the PNG rings and the interactive overlay rings line up; otherwise\n\t\t// a smaller PNG ring sits inside the larger overlay ring and looks like\n\t\t// a stray dot at the center.\n\t\tconst dotRadius = Math.max(this.settings.width, this.settings.height) / 80\n\t\t// Resolve case/control colors via the shared helper (see colors.ts) so the\n\t\t// PNG and the SVG overlay paint each side with the exact same hex string.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\treturn {\n\t\t\tsignificanceThresholds: {\n\t\t\t\tpValueCutoff: this.settings.pValue,\n\t\t\t\tpValueType: this.settings.pValueType,\n\t\t\t\tfoldChangeCutoff: this.settings.foldChangeCutoff\n\t\t\t},\n\t\t\tpixelWidth: this.settings.width,\n\t\t\tpixelHeight: this.settings.height,\n\t\t\tcolorSignificant: toHex(this.settings.defaultSignColor, 'red'),\n\t\t\tcolorSignificantUp: caseColor,\n\t\t\tcolorSignificantDown: controlColor,\n\t\t\tcolorNonsignificant: toHex(this.settings.defaultNonSignColor, 'black'),\n\t\t\tdotRadius,\n\t\t\tmaxInteractiveDots: this.settings.maxInteractiveDots,\n\t\t\t// Render the PNG at device-pixel resolution so it stays sharp on\n\t\t\t// retina screens. The server reports the plot extent in CSS-space,\n\t\t\t// so SVG overlay coords are unaffected.\n\t\t\t//\n\t\t\t// Oversample by 2\u00D7 so the PNG also stays sharp when the user\n\t\t\t// *zooms in after* the initial render (the captured DPR is frozen\n\t\t\t// at fetch time \u2014 bigger headroom = more tolerable post-render\n\t\t\t// zoom before pixelation appears). The server clamp keeps the\n\t\t\t// bitmap memory bounded.\n\t\t\tdevicePixelRatio: (typeof window !== 'undefined' ? window.devicePixelRatio : 1) * 2\n\t\t}\n\t}\n\n\t//This is a workaround until the server can accept an arr of confounder tws\n\taddConfounderTw(body) {\n\t\tconst confounders = this.config?.confounderTws\n\t\tif (confounders?.length) {\n\t\t\tbody.tw = this.config.confounderTws[0]\n\t\t\tif (confounders.length > 1) body.tw2 = this.config.confounderTws[1]\n\t\t}\n\t}\n\n\t//Single cell cell type\n\tgetSCCTRequestBody(): TermdbSingleCellDEgenesRequest {\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsample: this.config.sample,\n\t\t\ttermId: this.config.termId,\n\t\t\tcategoryName: this.config.categoryName,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t\treturn body\n\t}\n\n\tgetDapRequestBody() {\n\t\tconst { organism, assay, cohort } = this.config.proteomeDetails\n\t\treturn {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\torganism,\n\t\t\tassay,\n\t\t\tcohort,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t}\n\n\t/** retrieve the sampleId/sampleName for samples in\n\t * the \"others\" group instead of using {in: false} */\n\tasync getOtherSamples(samplelst) {\n\t\tconst othersSamplesGroup = samplelst.groups.find(g => !g.in)\n\t\tif (!othersSamplesGroup) return\n\n\t\tconst state = this.app.getState()\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tothersSamplesGroup.values = []\n\t\t// retrieve full list of samples based on current filter. put samples not in samplesGroup in \"others\" group\n\t\tfor (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {\n\t\t\t// s={id,name}, samplelst.groups[].values[]={sampleId,sample}\n\t\t\tif (samplesGroup.values.indexOf(i => i.sampleId == s.id) == -1) {\n\t\t\t\tothersSamplesGroup.values.push({ sampleId: s.id, sample: s.name })\n\t\t\t}\n\t\t}\n\t\tothersSamplesGroup.in = true\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-M66VDGSH.js

@@ -0,0 +1,272 @@
+import {
+  fillbar,
+  make_table_2col
+} from "./chunk-TKW5TW4Z.js";
+
+// src/block.mds.expressionstat.js
+var color_noinfo = "#858585";
+function init_config(cfg) {
+  if (!cfg.datatype) cfg.datatype = "FPKM";
+  if (!cfg.itemcolor) cfg.itemcolor = "green";
+  if (!cfg.ase) cfg.ase = {};
+  if (cfg.ase.qvalue == void 0) cfg.ase.qvalue = 0.05;
+  if (cfg.ase.meandelta_monoallelic == void 0) cfg.ase.meandelta_monoallelic = 0.3;
+  if (cfg.ase.asemarkernumber_biallelic == void 0) cfg.ase.asemarkernumber_biallelic = 0;
+  if (!cfg.ase.color_noinfo) cfg.ase.color_noinfo = color_noinfo;
+  if (!cfg.ase.color_uncertain) cfg.ase.color_uncertain = "#A8E0B5";
+  if (!cfg.ase.color_biallelic) cfg.ase.color_biallelic = "#40859C";
+  if (!cfg.ase.color_monoallelic) cfg.ase.color_monoallelic = "#d95f02";
+  if (!cfg.outlier) cfg.outlier = {};
+  if (cfg.outlier.pvalue_cutoff == void 0) cfg.outlier.pvalue_cutoff = 0.05;
+  if (cfg.outlier.rank_asehigh_cutoff == void 0) cfg.outlier.rank_asehigh_cutoff = 0.1;
+  if (!cfg.outlier.color_outlier) cfg.outlier.color_outlier = "#FF8875";
+  if (!cfg.outlier.color_outlier_asehigh) cfg.outlier.color_outlier_asehigh = "blue";
+}
+function measure(v, cfg) {
+  if (!cfg) return;
+  v.estat = {};
+  if (v.ase && cfg.ase) {
+    const qvalue = v.ase.qvalue || v.ase.geometricmean;
+    if (qvalue == void 0) {
+      v.estat.ase_noinfo = true;
+    } else if (qvalue <= cfg.ase.qvalue) {
+      if (v.ase.mean_delta >= cfg.ase.meandelta_monoallelic) {
+        v.estat.ase_monoallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    } else {
+      if (v.ase.ase_markers == cfg.ase.asemarkernumber_biallelic) {
+        v.estat.ase_biallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    }
+  } else {
+    v.estat.ase_noinfo = true;
+  }
+  if (v.outlier && cfg.outlier) {
+    if (v.outlier.test_whitelist) {
+      if (v.outlier.test_whitelist.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_whitelist.rank) && Number.isInteger(v.outlier.test_whitelist.size) && v.outlier.test_whitelist.rank / v.outlier.test_whitelist.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_whitelist.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_biallelic) {
+      if (v.outlier.test_biallelic.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_biallelic.rank) && Number.isInteger(v.outlier.test_biallelic.size) && v.outlier.test_biallelic.rank / v.outlier.test_biallelic.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_biallelic.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_entirecohort) {
+      if (v.outlier.test_entirecohort.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_entirecohort.rank) && Number.isInteger(v.outlier.test_entirecohort.size) && v.outlier.test_entirecohort.rank / v.outlier.test_entirecohort.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_entirecohort.asehigh = true;
+          }
+        }
+      }
+    }
+  }
+}
+function showsingleitem_table(v, cfg, table) {
+  if (!v.estat) return;
+  if (cfg.no_ase) return;
+  if (v.ase) {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 2).style("background", ase_color(v, cfg)).style("color", "white").html(
+      (v.estat.ase_monoallelic ? "Mono-allelic" : v.estat.ase_biallelic ? "Bi-allelic" : "ASE uncertain") + "<br>(allele-specific expression)"
+    );
+    const lst = [
+      {
+        k: "#SNPs heterozygous in DNA",
+        v: v.ase.markers
+      },
+      {
+        k: "#SNPs showing ASE in RNA",
+        v: v.ase.ase_markers
+      },
+      {
+        k: "Mean delta of ASE SNPs",
+        v: v.ase.mean_delta
+      }
+    ];
+    if (v.ase.qvalue) {
+      lst.push({
+        k: "Q-value",
+        v: v.ase.qvalue
+      });
+    } else if (v.ase.geometricmean) {
+      lst.push({
+        k: "Geometric mean of binomial P-values of ASE SNPs",
+        v: v.ase.geometricmean
+      });
+    }
+    const td = tr.append("td");
+    make_table_2col(td, lst);
+  } else {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 3).style("background", cfg.ase.color_noinfo).style("color", "white").text("No info on allele-specific expression");
+  }
+  if (v.snps && v.snps.length > 0) {
+    const hetsnp = v.snps.filter((i) => i.dnacount && i.dnacount.ishet);
+    if (hetsnp.length > 0) {
+      const lst = [];
+      for (const m of hetsnp) {
+        lst.push(
+          "<tr><td>" + m.chr + ":" + (m.pos + 1) + " " + m.ref + ">" + m.alt + "</td><td>" + fillbar(null, { f: m.dnacount.f }) + " " + m.dnacount.ref + "/" + m.dnacount.alt + "</td><td>" + (m.rnacount.nocoverage ? '<span style="font-size:.8em;opacity:.5">No coverage</span>' : fillbar(null, { f: m.rnacount.f }) + " " + m.rnacount.ref + "/" + m.rnacount.alt) + "</td><td>" + (m.rnacount.pvalue || "-") + "</td></tr>"
+        );
+      }
+      table.append("tr").append("td").attr("colspan", 3).html(
+        '<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;"><tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>' + lst.join("") + "</table>"
+      );
+    }
+  }
+  if (v.outlier) {
+    if (v.outlier.test_whitelist) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (white list)");
+      const lst = [];
+      for (const k in v.outlier.test_whitelist) {
+        lst.push({ k, v: v.outlier.test_whitelist[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_whitelist.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_biallelic) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (biallelic)");
+      const lst = [];
+      for (const k in v.outlier.test_biallelic) {
+        lst.push({ k, v: v.outlier.test_biallelic[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_biallelic.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_entirecohort) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (all samples)");
+      const lst = [];
+      for (const k in v.outlier.test_entirecohort) {
+        lst.push({ k, v: v.outlier.test_entirecohort[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_entirecohort.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+  }
+}
+function ase_color(v, cfg) {
+  if (cfg.no_ase) return color_noinfo;
+  if (!cfg.ase) return color_noinfo;
+  if (!v.estat) return cfg.ase.color_noinfo;
+  if (v.estat.ase_monoallelic) return cfg.ase.color_monoallelic;
+  if (v.estat.ase_biallelic) return cfg.ase.color_biallelic;
+  if (v.estat.ase_uncertain) return cfg.ase.color_uncertain;
+  return cfg.ase.color_noinfo;
+}
+function ui_config(holder, cfg, tk, call) {
+  const indent = 30;
+  {
+    const row = holder.append("div").style("margin-bottom", "5px");
+    row.append("span").html("If " + (tk.checkrnabam ? "p-value geometric mean" : "Q-VALUE") + " &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.qvalue).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.qvalue == v) {
+        return;
+      }
+      cfg.ase.qvalue = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:");
+  }
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If MEAN_DELTA &ge;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.meandelta_monoallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.meandelta_monoallelic == v) {
+        return;
+      }
+      cfg.ase.meandelta_monoallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_monoallelic + ';padding:1px 5px;color:white;">mono-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px 0px").html("Else:");
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If number of ASE markers &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.asemarkernumber_biallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseInt(event.target.value);
+      if (v < 0) {
+        return;
+      }
+      if (cfg.ase.asemarkernumber_biallelic == v) {
+        return;
+      }
+      cfg.ase.asemarkernumber_biallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_biallelic + ';padding:1px 5px;color:white;">bi-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "10px").append("button").text("Default ASE parameters").on("click", () => {
+    cfg.ase.qvalue = 0.05;
+    cfg.ase.meandelta_monoallelic = 0.3;
+    cfg.ase.asemarkernumber_biallelic = 0;
+    call();
+  });
+}
+
+export {
+  init_config,
+  measure,
+  showsingleitem_table,
+  ase_color,
+  ui_config
+};
+//# sourceMappingURL=chunk-M66VDGSH.js.map