@platforma-open/milaboratories.tcrdisco-enrichment.model 1.1.0

package/dist/index.js

@@ -0,0 +1,306 @@
+import { BlockModel, createPlDataTableStateV2, isPColumnSpec, createPlDataTableV2, getUniquePartitionKeys, createPlDataTableSheet, createPFrameForGraphs } from "@platforma-sdk/model";
+function filterPCols(pCols) {
+  pCols = pCols.filter(
+    (col) => col.spec.name === "pl7.app/differentialTCRAbundance/log2foldchange" || col.spec.name === "pl7.app/differentialTCRAbundance/minlog10padj" || col.spec.name === "pl7.app/differentialTCRAbundance/regulationDirection" || col.spec.name === "pl7.app/differentialTCRAbundance/contrastGroup" || col.spec.name === "pl7.app/differentialTCRAbundance/chain" || col.spec.name === "pl7.app/differentialTCRAbundance/cdsubset" || col.spec.name === "pl7.app/differentialTCRAbundance/robustEnrichment"
+  );
+  return pCols;
+}
+const model = BlockModel.create().withArgs({
+  covariateRefs: [],
+  numerators: [],
+  denominators: [],
+  findTcrAbPairs: false,
+  thresholdCounts: 10,
+  thresholdSamples: 3,
+  log2FcThreshold: 0,
+  pAdjThreshold: 0.05
+}).withUiState({
+  title: "TCR Disco",
+  tableState: createPlDataTableStateV2(),
+  pairsTableState: createPlDataTableStateV2(),
+  selectedChain: "alpha",
+  cdSubsetColValid: false,
+  graphState: {
+    title: "Volcano plot",
+    template: "dots",
+    currentTab: null
+  },
+  pairsHeatmapState: {
+    title: "TCR A/B pairs correlation heatmap",
+    template: "heatmapClustered",
+    layersSettings: {
+      heatmapClustered: {
+        dendrogramX: false,
+        dendrogramY: false
+      }
+    },
+    axesSettings: {
+      axisX: {
+        cellSize: 20
+      },
+      axisY: {
+        cellSize: 20
+      }
+    }
+  },
+  frequenciesHeatmapState: {
+    title: "Enriched clonotypes heatmap",
+    template: "heatmapClustered",
+    layersSettings: {
+      heatmapClustered: {
+        normalizationDirection: "row",
+        normalizationMethod: "standardScaling",
+        dendrogramX: false,
+        dendrogramY: false
+      }
+    },
+    axesSettings: {
+      axisX: {
+        cellSize: 20
+      },
+      axisY: {
+        cellSize: 20
+      }
+    }
+  },
+  alignmentModel: {}
+}).argsValid((ctx) => {
+  var _a;
+  return ctx.args.mainRef !== void 0 && ctx.args.covariateRefs !== void 0 && ctx.args.contrastFactor !== void 0 && ctx.args.numerators.length > 0 && ctx.args.denominators.length > 0 && ctx.args.log2FcThreshold !== void 0 && ctx.args.pAdjThreshold !== void 0 && ctx.args.thresholdCounts !== void 0 && ctx.args.thresholdSamples !== void 0 && (!ctx.args.cdRef || ctx.args.cdSubsetCol !== void 0 && ((_a = ctx.uiState) == null ? void 0 : _a.cdSubsetColValid));
+}).output("inputOptions", (ctx) => {
+  return ctx.resultPool.getOptions([
+    {
+      axes: [
+        { name: "pl7.app/sampleId" },
+        {
+          domain: {
+            "pl7.app/vdj/chain": "TCRAlpha"
+          }
+        }
+      ],
+      annotations: {
+        "pl7.app/isAbundance": "true",
+        "pl7.app/abundance/normalized": "false",
+        "pl7.app/abundance/isPrimary": "true"
+      }
+    }
+  ], {
+    label: {
+      includeNativeLabel: false,
+      addLabelAsSuffix: true,
+      forceTraceElements: []
+    },
+    refsWithEnrichments: false
+  });
+}).output(
+  "metadataOptions",
+  (ctx) => ctx.resultPool.getOptions((spec) => isPColumnSpec(spec) && spec.name === "pl7.app/metadata")
+).output("denominatorOptions", (ctx) => {
+  if (!ctx.args.contrastFactor) return void 0;
+  const pColumn = ctx.resultPool.getPColumnByRef(ctx.args.contrastFactor);
+  if (!pColumn) return void 0;
+  return ctx.createPFrame([pColumn]);
+}).output("cdSubsetOptions", (ctx) => {
+  if (!ctx.args.cdSubsetCol) return void 0;
+  const pColumn = ctx.resultPool.getPColumnByRef(ctx.args.cdSubsetCol);
+  if (!pColumn) return void 0;
+  return ctx.createPFrame([pColumn]);
+}).output("barcodeColPresent", (ctx) => {
+  const metadataCols = ctx.resultPool.selectColumns(
+    (spec) => spec.name === "pl7.app/metadata"
+  );
+  if (metadataCols === void 0) {
+    return false;
+  }
+  return metadataCols.some((col) => {
+    var _a;
+    return ((_a = col.spec.annotations) == null ? void 0 : _a["pl7.app/label"]) === "Barcode ID";
+  });
+}).output("pt", (ctx) => {
+  var _a, _b, _c, _d;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "topDegPFAlpha" : "topDegPFBeta";
+  const pCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  return createPlDataTableV2(ctx, pCols, (_d = ctx.uiState) == null ? void 0 : _d.tableState);
+}).output("sheets", (ctx) => {
+  var _a, _b, _c, _d;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "topDegPFAlpha" : "topDegPFBeta";
+  const pCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (pCols === void 0 || pCols.length === 0) {
+    return void 0;
+  }
+  const partitionKeys = (_d = getUniquePartitionKeys(pCols[0].data)) == null ? void 0 : _d[0];
+  if (!partitionKeys) return void 0;
+  return [createPlDataTableSheet(ctx, pCols[0].spec.axesSpec[0], partitionKeys)];
+}).output("pairsPt", (ctx) => {
+  var _a, _b, _c;
+  const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve({ field: "pairsPF", allowPermanentAbsence: true })) == null ? void 0 : _b.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  return createPlDataTableV2(ctx, pCols, (_c = ctx.uiState) == null ? void 0 : _c.pairsTableState);
+}).output("pairsSheets", (ctx) => {
+  var _a, _b, _c;
+  const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve({ field: "pairsPF", allowPermanentAbsence: true })) == null ? void 0 : _b.getPColumns();
+  if (pCols === void 0 || pCols.length === 0) {
+    return void 0;
+  }
+  const partitionKeys = (_c = getUniquePartitionKeys(pCols[0].data)) == null ? void 0 : _c[0];
+  if (!partitionKeys) return void 0;
+  return [createPlDataTableSheet(ctx, pCols[0].spec.axesSpec[0], partitionKeys)];
+}).output("topTablePf", (ctx) => {
+  var _a, _b, _c;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "topDegPFAlpha" : "topDegPFBeta";
+  let pCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  pCols = filterPCols(pCols);
+  return createPFrameForGraphs(ctx, pCols);
+}).output("topTablePcols", (ctx) => {
+  var _a, _b, _c;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "topDegPFAlpha" : "topDegPFBeta";
+  const pCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  return pCols.map(
+    (c) => ({
+      columnId: c.id,
+      spec: c.spec
+    })
+  );
+}).output("pairsHeatmapPf", (ctx) => {
+  var _a, _b;
+  const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve({ field: "pairsPF", allowPermanentAbsence: true })) == null ? void 0 : _b.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  let filteredPcols = pCols.filter((col) => col.spec.name !== "pl7.app/differentialTCRAbundance/tra_CDR3aa" && col.spec.name !== "pl7.app/differentialTCRAbundance/trb_CDR3aa" && col.spec.name !== "pl7.app/differentialTCRAbundance/tra_VGene" && col.spec.name !== "pl7.app/differentialTCRAbundance/trb_VGene");
+  const cdr3Pcols = ctx.resultPool.selectColumns(
+    (spec) => {
+      var _a2, _b2;
+      return spec.name === "pl7.app/vdj/sequence" && ((_a2 = spec.domain) == null ? void 0 : _a2["pl7.app/alphabet"]) === "aminoacid" && ((_b2 = spec.domain) == null ? void 0 : _b2["pl7.app/vdj/feature"]) === "CDR3";
+    }
+  );
+  const vGenePcols = ctx.resultPool.selectColumns(
+    (spec) => {
+      var _a2, _b2;
+      return spec.name === "pl7.app/vdj/sequence" && ((_a2 = spec.domain) == null ? void 0 : _a2["pl7.app/alphabet"]) === "aminoacid" && ((_b2 = spec.domain) == null ? void 0 : _b2["pl7.app/vdj/feature"]) === "VGene";
+    }
+  );
+  if (cdr3Pcols !== void 0 && vGenePcols !== void 0) {
+    filteredPcols = [...filteredPcols, ...cdr3Pcols, ...vGenePcols];
+  }
+  const clonotypeIds = ctx.resultPool.selectColumns(
+    (spec) => {
+      var _a2;
+      return spec.name === "pl7.app/label" && ((_a2 = spec.axesSpec) == null ? void 0 : _a2.some((axis) => axis.name === "pl7.app/vdj/clonotypeKey" || axis.name === "pl7.app/vdj/scClonotypeKey"));
+    }
+  );
+  const allPcols = [...filteredPcols, ...clonotypeIds];
+  return ctx.createPFrame(allPcols);
+}).output("pairsHeatmapPcols", (ctx) => {
+  var _a, _b;
+  const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve({ field: "pairsPF", allowPermanentAbsence: true })) == null ? void 0 : _b.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  let filteredPcols = pCols.filter((col) => col.spec.name !== "pl7.app/differentialTCRAbundance/tra_CDR3aa" && col.spec.name !== "pl7.app/differentialTCRAbundance/trb_CDR3aa" && col.spec.name !== "pl7.app/differentialTCRAbundance/tra_VGene" && col.spec.name !== "pl7.app/differentialTCRAbundance/trb_VGene");
+  const cdr3Pcols = ctx.resultPool.selectColumns(
+    (spec) => {
+      var _a2, _b2;
+      return spec.name === "pl7.app/vdj/sequence" && ((_a2 = spec.domain) == null ? void 0 : _a2["pl7.app/alphabet"]) === "aminoacid" && ((_b2 = spec.domain) == null ? void 0 : _b2["pl7.app/vdj/feature"]) === "CDR3";
+    }
+  );
+  if (cdr3Pcols !== void 0) {
+    filteredPcols = [...filteredPcols, ...cdr3Pcols];
+  }
+  return filteredPcols.map(
+    (c) => ({
+      columnId: c.id,
+      spec: c.spec
+    })
+  );
+}).output("frequenciesHeatmapPf", (ctx) => {
+  var _a, _b, _c, _d, _e;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "mainAlphaFrequenciesPF" : "mainBetaFrequenciesPF";
+  let allPcols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (allPcols === void 0) {
+    return void 0;
+  }
+  const subtypeLabel = selectedChain === "alpha" ? "clonotypeToSubsetAlpha" : "clonotypeToSubsetBeta";
+  const clonotypeToSubsetPcols = (_e = (_d = ctx.outputs) == null ? void 0 : _d.resolve({ field: subtypeLabel, allowPermanentAbsence: true })) == null ? void 0 : _e.getPColumns();
+  if (clonotypeToSubsetPcols !== void 0) {
+    allPcols = [...allPcols, ...clonotypeToSubsetPcols];
+  }
+  return createPFrameForGraphs(ctx, allPcols);
+}).output("frequenciesHeatmapPcols", (ctx) => {
+  var _a, _b, _c, _d, _e;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "mainAlphaFrequenciesPF" : "mainBetaFrequenciesPF";
+  const pCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (pCols === void 0) {
+    return void 0;
+  }
+  const subtypeLabel = selectedChain === "alpha" ? "clonotypeToSubsetAlpha" : "clonotypeToSubsetBeta";
+  const clonotypeToSubsetPcols = (_e = (_d = ctx.outputs) == null ? void 0 : _d.resolve({ field: subtypeLabel, allowPermanentAbsence: true })) == null ? void 0 : _e.getPColumns();
+  const metadataCols = ctx.resultPool.selectColumns(
+    (spec) => spec.name === "pl7.app/metadata"
+  );
+  const chain = selectedChain === "alpha" ? "TCRAlpha" : "TCRBeta";
+  const sequenceCol = ctx.resultPool.selectColumns(
+    (spec) => {
+      var _a2, _b2, _c2;
+      return spec.name === "pl7.app/vdj/sequence" && ((_a2 = spec.domain) == null ? void 0 : _a2["pl7.app/alphabet"]) === "aminoacid" && ((_b2 = spec.domain) == null ? void 0 : _b2["pl7.app/vdj/feature"]) === "CDR3" && ((_c2 = spec.axesSpec[0].domain) == null ? void 0 : _c2["pl7.app/vdj/chain"]) === chain;
+    }
+  );
+  let allCols = [...pCols, ...metadataCols];
+  if (clonotypeToSubsetPcols !== void 0) {
+    allCols = [...allCols, ...clonotypeToSubsetPcols];
+  }
+  if (sequenceCol !== void 0) {
+    allCols = [...allCols, ...sequenceCol];
+  }
+  return allCols.map(
+    (c) => ({
+      columnId: c.id,
+      spec: c.spec
+    })
+  );
+}).output("msaPf", (ctx) => {
+  var _a, _b, _c;
+  const selectedChain = ((_a = ctx.uiState) == null ? void 0 : _a.selectedChain) ?? "alpha";
+  const outputName = selectedChain === "alpha" ? "topDegPFAlpha" : "topDegPFBeta";
+  const msaCols = (_c = (_b = ctx.outputs) == null ? void 0 : _b.resolve(outputName)) == null ? void 0 : _c.getPColumns();
+  if (!msaCols) return void 0;
+  const datasetRef = ctx.args.mainRef;
+  if (datasetRef === void 0)
+    return void 0;
+  return createPFrameForGraphs(ctx, msaCols);
+}).title((ctx) => {
+  var _a;
+  return ((_a = ctx.uiState) == null ? void 0 : _a.title) ?? "TCR Disco";
+}).sections((ctx) => {
+  const sections = [
+    { type: "link", href: "/", label: "Main" },
+    { type: "link", href: "/graph", label: "Volcano plot" },
+    { type: "link", href: "/freq-heatmap", label: "Enriched clonotypes heatmap" }
+  ];
+  if (ctx.args.findTcrAbPairs) {
+    sections.push({ type: "link", href: "/pairs", label: "TCR AB Pairs" });
+    sections.push({ type: "link", href: "/pairs-heatmap", label: "Pairs correlation heatmap" });
+  }
+  return sections;
+}).done(2);
+export {
+  model
+};
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sources":["../src/index.ts"],"sourcesContent":["import type { GraphMakerState } from '@milaboratories/graph-maker';\nimport type {\n  InferOutputsType,\n  PColumn,\n  PColumnDataUniversal,\n  PColumnIdAndSpec,\n  PFrameHandle,\n  PlDataTableStateV2,\n  PlMultiSequenceAlignmentModel,\n  PlRef,\n  TreeNodeAccessor,\n} from '@platforma-sdk/model';\nimport {\n  BlockModel,\n  createPFrameForGraphs,\n  createPlDataTableSheet,\n  createPlDataTableStateV2,\n  createPlDataTableV2,\n  getUniquePartitionKeys,\n  isPColumnSpec,\n} from '@platforma-sdk/model';\n\nexport type UiState = {\n  tableState: PlDataTableStateV2;\n  pairsTableState: PlDataTableStateV2;\n  title?: string;\n  selectedChain?: 'alpha' | 'beta';\n  cdSubsetColValid: boolean;\n  graphState: GraphMakerState;\n  pairsHeatmapState: GraphMakerState;\n  frequenciesHeatmapState: GraphMakerState;\n  alignmentModel: PlMultiSequenceAlignmentModel;\n};\n\nexport type BlockArgs = {\n  name?: string;\n  mainRef?: PlRef;\n  cdRef?: PlRef;\n  cdSubsetCol?: PlRef;\n  pairingMetadataCol?: string;\n  covariateRefs: PlRef[];\n  contrastFactor?: PlRef;\n  numerators: string[];\n  denominators: string[];\n  findTcrAbPairs: boolean;\n  thresholdCounts: number;\n  thresholdSamples: number;\n  log2FcThreshold: number;\n  pAdjThreshold: number;\n};\n\n// Filter columns for volcano plot\nfunction filterPCols(\n  pCols: PColumn<TreeNodeAccessor>[]):\n  PColumn<TreeNodeAccessor>[] {\n  // Allow only log2 FC and -log10 Padjust as options for volcano axis\n  pCols = pCols.filter(\n    (col) => col.spec.name === 'pl7.app/differentialTCRAbundance/log2foldchange'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/minlog10padj'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/regulationDirection'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/contrastGroup'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/chain'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/cdsubset'\n      || col.spec.name === 'pl7.app/differentialTCRAbundance/robustEnrichment',\n  );\n  return pCols;\n}\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    covariateRefs: [],\n    numerators: [],\n    denominators: [],\n    findTcrAbPairs: false,\n    thresholdCounts: 10,\n    thresholdSamples: 3,\n    log2FcThreshold: 0,\n    pAdjThreshold: 0.05,\n  })\n\n  .withUiState<UiState>({\n    title: 'TCR Disco',\n    tableState: createPlDataTableStateV2(),\n    pairsTableState: createPlDataTableStateV2(),\n    selectedChain: 'alpha',\n    cdSubsetColValid: false,\n    graphState: {\n      title: 'Volcano plot',\n      template: 'dots',\n      currentTab: null,\n    },\n    pairsHeatmapState: {\n      title: 'TCR A/B pairs correlation heatmap',\n      template: 'heatmapClustered',\n      layersSettings: {\n        heatmapClustered: {\n          dendrogramX: false,\n          dendrogramY: false,\n        },\n      },\n      axesSettings: {\n        axisX: {\n          cellSize: 20,\n        },\n        axisY: {\n          cellSize: 20,\n        },\n      },\n    },\n    frequenciesHeatmapState: {\n      title: 'Enriched clonotypes heatmap',\n      template: 'heatmapClustered',\n      layersSettings: {\n        heatmapClustered: {\n          normalizationDirection: 'row',\n          normalizationMethod: 'standardScaling',\n          dendrogramX: false,\n          dendrogramY: false,\n        },\n      },\n      axesSettings: {\n        axisX: {\n          cellSize: 20,\n        },\n        axisY: {\n          cellSize: 20,\n        },\n      },\n    },\n    alignmentModel: {},\n  })\n\n  .argsValid((ctx) => (\n    ((ctx.args.mainRef !== undefined)\n      && (ctx.args.covariateRefs !== undefined)\n      && (ctx.args.contrastFactor !== undefined)\n      && (ctx.args.numerators.length > 0)\n      && (ctx.args.denominators.length > 0)\n      && (ctx.args.log2FcThreshold !== undefined)\n      && (ctx.args.pAdjThreshold !== undefined)\n      && (ctx.args.thresholdCounts !== undefined)\n      && (ctx.args.thresholdSamples !== undefined)\n      && (!ctx.args.cdRef || (ctx.args.cdSubsetCol !== undefined && ctx.uiState?.cdSubsetColValid)))\n  ))\n\n  // Allow user to choose Alpha chain, will pick beta if available\n  // @TODO: Should we allow single analysis of beta chain?\n  .output('inputOptions', (ctx) => {\n    return ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { domain: {\n          'pl7.app/vdj/chain': 'TCRAlpha',\n        },\n        },\n      ],\n      annotations: { 'pl7.app/isAbundance': 'true',\n        'pl7.app/abundance/normalized': 'false',\n        'pl7.app/abundance/isPrimary': 'true',\n      },\n    },\n    ], { label: { includeNativeLabel: false, addLabelAsSuffix: true,\n      forceTraceElements: [],\n    },\n    refsWithEnrichments: false });\n  })\n\n  .output('metadataOptions', (ctx) =>\n    ctx.resultPool.getOptions((spec) => isPColumnSpec(spec) && spec.name === 'pl7.app/metadata'),\n  )\n\n  .output('denominatorOptions', (ctx) => {\n    if (!ctx.args.contrastFactor) return undefined;\n\n    const pColumn = ctx.resultPool.getPColumnByRef(ctx.args.contrastFactor);\n    if (!pColumn) return undefined;\n\n    return ctx.createPFrame([pColumn]);\n  })\n\n  .output('cdSubsetOptions', (ctx) => {\n    if (!ctx.args.cdSubsetCol) return undefined;\n\n    const pColumn = ctx.resultPool.getPColumnByRef(ctx.args.cdSubsetCol);\n    if (!pColumn) return undefined;\n\n    return ctx.createPFrame([pColumn]);\n  })\n\n  // Check if \"Barcode ID\" column is present in metadata, otherwise return false\n  // This column will be present in demultiplexed data and will relate same\n  // samples from different chains\n  .output('barcodeColPresent', (ctx) => {\n    const metadataCols = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/metadata',\n    );\n    if (metadataCols === undefined) {\n      return false;\n    }\n    return metadataCols.some((col) => col.spec.annotations?.['pl7.app/label'] === 'Barcode ID');\n  })\n\n  .output('pt', (ctx) => {\n    const selectedChain = ctx.uiState?.selectedChain ?? 'alpha';\n    const outputName = selectedChain === 'alpha' ? 'topDegPFAlpha' : 'topDegPFBeta';\n    const pCols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    return createPlDataTableV2(ctx, pCols, ctx.uiState?.tableState);\n  })\n\n  .output('sheets', (ctx) => {\n    const selectedChain = ctx.uiState?.selectedChain ?? 'alpha';\n    const outputName = selectedChain === 'alpha' ? 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'alpha';\n    const outputName = selectedChain === 'alpha' ? 'topDegPFAlpha' : 'topDegPFBeta';\n    let pCols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    pCols = filterPCols(pCols);\n\n    return createPFrameForGraphs(ctx, pCols);\n  })\n\n  .output('topTablePcols', (ctx) => {\n    const selectedChain = ctx.uiState?.selectedChain ?? 'alpha';\n    const outputName = selectedChain === 'alpha' ? 'topDegPFAlpha' : 'topDegPFBeta';\n    const pCols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    return pCols.map(\n      (c) =>\n        ({\n          columnId: c.id,\n          spec: c.spec,\n        } satisfies PColumnIdAndSpec),\n    );\n  })\n\n  .output('pairsHeatmapPf', (ctx): PFrameHandle | undefined => {\n    const pCols = ctx.outputs?.resolve({ field: 'pairsPF', allowPermanentAbsence: true })?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    // Filter out CDR3 and Vgene columns\n    let filteredPcols = pCols.filter((col) => col.spec.name !== 'pl7.app/differentialTCRAbundance/tra_CDR3aa'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/trb_CDR3aa'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/tra_VGene'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/trb_VGene');\n\n    // Get from the pool CDR3 aa and VGene pcolumns\n    const cdr3Pcols = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/vdj/sequence'\n        && spec.domain?.['pl7.app/alphabet'] === 'aminoacid'\n        && spec.domain?.['pl7.app/vdj/feature'] === 'CDR3',\n    );\n    const vGenePcols = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/vdj/sequence'\n        && spec.domain?.['pl7.app/alphabet'] === 'aminoacid'\n        && spec.domain?.['pl7.app/vdj/feature'] === 'VGene',\n    );\n\n    if (cdr3Pcols !== undefined && vGenePcols !== undefined) {\n      filteredPcols = [...filteredPcols, ...cdr3Pcols, ...vGenePcols] as PColumn<TreeNodeAccessor>[];\n    }\n\n    // Add sample ID to labels information\n    const clonotypeIds = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/label'\n        && spec.axesSpec?.some((axis) => axis.name === 'pl7.app/vdj/clonotypeKey' || axis.name === 'pl7.app/vdj/scClonotypeKey'),\n    ) as PColumn<PColumnDataUniversal>[];\n\n    const allPcols = [...filteredPcols, ...clonotypeIds];\n\n    return ctx.createPFrame(allPcols);\n  })\n\n  .output('pairsHeatmapPcols', (ctx) => {\n    const pCols = ctx.outputs?.resolve({ field: 'pairsPF', allowPermanentAbsence: true })?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    // Filter out CDR3 and Vgene columns\n    let filteredPcols = pCols.filter((col) => col.spec.name !== 'pl7.app/differentialTCRAbundance/tra_CDR3aa'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/trb_CDR3aa'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/tra_VGene'\n      && col.spec.name !== 'pl7.app/differentialTCRAbundance/trb_VGene');\n\n    // Get from the pool CDR3 aa and VGene pcolumns\n    const cdr3Pcols = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/vdj/sequence'\n        && spec.domain?.['pl7.app/alphabet'] === 'aminoacid'\n        && spec.domain?.['pl7.app/vdj/feature'] === 'CDR3',\n    );\n    if (cdr3Pcols !== undefined) {\n      filteredPcols = [...filteredPcols, ...cdr3Pcols] as PColumn<TreeNodeAccessor>[];\n    }\n    return filteredPcols.map(\n      (c) =>\n        ({\n          columnId: c.id,\n          spec: c.spec,\n        } satisfies PColumnIdAndSpec),\n    );\n  })\n\n  .output('frequenciesHeatmapPf', (ctx): PFrameHandle | undefined => {\n    const selectedChain = ctx.uiState?.selectedChain ?? 'alpha';\n    const outputName = selectedChain === 'alpha' ? 'mainAlphaFrequenciesPF' : 'mainBetaFrequenciesPF';\n    let allPcols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (allPcols === undefined) {\n      return undefined;\n    }\n\n    // Get all metadata columns that are compatible with the Sample axis\n    // const sampleIds = ctx.resultPool.selectColumns(\n    //   (spec) => spec.name === 'pl7.app/label'\n    //     && spec.axesSpec?.some((axis) => axis.name === 'pl7.app/sampleId'\n    //       || axis.name === 'pl7.app/vdj/clonotypeKey'\n    //       || axis.name === 'pl7.app/vdj/scClonotypeKey'\n    //       || axis.name === 'pl7.app/metadata'),\n    // ) as PColumn<PColumnDataUniversal>[];\n\n    // let allPcols = [...pCols, ...sampleIds];\n    // let allPcols = pCols;\n\n    const subtypeLabel = selectedChain === 'alpha' ? 'clonotypeToSubsetAlpha' : 'clonotypeToSubsetBeta';\n    const clonotypeToSubsetPcols = ctx.outputs?.resolve({ field: subtypeLabel, allowPermanentAbsence: true })?.getPColumns();\n    if (clonotypeToSubsetPcols !== undefined) {\n      allPcols = [...allPcols, ...clonotypeToSubsetPcols];\n    }\n\n    // return ctx.createPFrame([...pCols, ...metadataCols]);\n    // return ctx.createPFrame(allPcols);\n    return createPFrameForGraphs(ctx, allPcols);\n  })\n\n  .output('frequenciesHeatmapPcols', (ctx) => {\n    const selectedChain = ctx.uiState?.selectedChain ?? 'alpha';\n    const outputName = selectedChain === 'alpha' ? 'mainAlphaFrequenciesPF' : 'mainBetaFrequenciesPF';\n    const pCols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    const subtypeLabel = selectedChain === 'alpha' ? 'clonotypeToSubsetAlpha' : 'clonotypeToSubsetBeta';\n    const clonotypeToSubsetPcols = ctx.outputs?.resolve({ field: subtypeLabel, allowPermanentAbsence: true })?.getPColumns();\n\n    // Get all metadata columns that are compatible with the Sample axis\n    const metadataCols = ctx.resultPool.selectColumns(\n      (spec) => spec.name === 'pl7.app/metadata',\n    );\n\n    // Get the sequence column for the sleected chain\n    const chain = selectedChain === 'alpha' ? 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'topDegPFAlpha' : 'topDegPFBeta';\n    const msaCols = ctx.outputs?.resolve(outputName)?.getPColumns();\n    if (!msaCols) return undefined;\n\n    const datasetRef = ctx.args.mainRef;\n    if (datasetRef === undefined)\n      return undefined;\n\n    return createPFrameForGraphs(ctx, msaCols);\n  })\n\n  .title((ctx) => ctx.uiState?.title ?? 'TCR Disco')\n\n  .sections((ctx) => {\n    const sections: Array<{ type: 'link'; href: `/${string}`; label: string }> = [\n      { type: 'link' as const, href: '/' as const, label: 'Main' },\n      { type: 'link' as const, href: '/graph' as const, label: 'Volcano plot' },\n      { type: 'link' as const, href: '/freq-heatmap' as const, label: 'Enriched clonotypes heatmap' },\n    ];\n\n    if (ctx.args.findTcrAbPairs) {\n      sections.push({ type: 'link' as const, href: '/pairs' as const, label: 'TCR AB Pairs' });\n      sections.push({ type: 'link' as const, href: '/pairs-heatmap' as const, label: 'Pairs correlation heatmap' });\n    }\n\n    return sections;\n  })\n\n  .done(2);\n\nexport type BlockOutputs = InferOutputsType<typeof 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