@platforma-open/milaboratories.humanization-score.model 0.3.0 → 0.3.2

package/dist/index.cjs

@@ -6,12 +6,8 @@ const defaultGraphStateHistogram = () => ({
 	title: "Humanness Score Distribution",
 	template: "bins",
 	currentTab: null,
-	axesSettings: { other: { binsCount: 20 } }
-});
-const defaultGraphStateBoxplot = () => ({
-	title: "Humanness by Sample",
-	template: "box",
-	currentTab: null
+	axesSettings: { other: { binsCount: 20 } },
+	layersSettings: { bins: { fillColor: "#2D93FA" } }
 });
 const inputSelectors = [{
 	axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/clonotypeKey" }],
@@ -23,13 +19,11 @@ const inputSelectors = [{
 const dataModel = new _platforma_sdk_model.DataModelBuilder().from("v1").upgradeLegacy(({ args, uiState }) => ({
 	...args,
 	tableState: uiState.tableState,
-	graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),
-	graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot()
+	graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram()
 })).init(() => ({
 	customBlockLabel: "",
 	tableState: (0, _platforma_sdk_model.createPlDataTableStateV2)(),
-	graphStateHistogram: defaultGraphStateHistogram(),
-	graphStateBoxplot: defaultGraphStateBoxplot()
+	graphStateHistogram: defaultGraphStateHistogram()
 }));
 const platforma = _platforma_sdk_model.BlockModelV3.create(dataModel).args((data) => {
 	if (!data.inputAnchor) throw new Error("Input anchor is required");
@@ -41,12 +35,14 @@ const platforma = _platforma_sdk_model.BlockModelV3.create(dataModel).args((data
 }).output("inputOptions", (ctx) => ctx.resultPool.getOptions(inputSelectors)).outputWithStatus("pt", (ctx) => {
 	const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
 	if (pCols === void 0) return;
+	const anchorCol = pCols[0];
+	if (anchorCol === void 0) return;
 	return (0, _platforma_sdk_model.createPlDataTableV3)(ctx, {
 		tableState: ctx.data.tableState,
-		columns: new _platforma_sdk_model.ArrayColumnProvider(pCols).getAllColumns().map((column) => ({
-			column,
-			isPrimary: true
-		}))
+		columns: {
+			anchors: { main: anchorCol.spec },
+			selector: { mode: "enrichment" }
+		}
 	});
 }).outputWithStatus("histogramPf", (ctx) => {
 	const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
@@ -59,72 +55,20 @@ const platforma = _platforma_sdk_model.BlockModelV3.create(dataModel).args((data
 		columnId: c.id,
 		spec: c.spec
 	}));
-}).outputWithStatus("perSamplePf", (ctx) => {
-	const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
-	if (humanness === void 0) return void 0;
-	const ref = ctx.data.inputAnchor;
-	if (ref === void 0) return void 0;
-	const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
-		axes: [{
-			anchor: "main",
-			idx: 0
-		}, {
-			anchor: "main",
-			idx: 1
-		}],
-		annotations: {
-			"pl7.app/isAbundance": "true",
-			"pl7.app/abundance/normalized": "false",
-			"pl7.app/abundance/isPrimary": "true"
-		}
-	}]);
-	return (0, _platforma_sdk_model.createPFrameForGraphs)(ctx, [...humanness, ...abundance ?? []]);
-}).output("perSamplePfPcols", (ctx) => {
-	const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
-	if (humanness === void 0 || humanness.length === 0) return void 0;
-	const ref = ctx.data.inputAnchor;
-	if (ref === void 0) return void 0;
-	const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
-		axes: [{
-			anchor: "main",
-			idx: 0
-		}, {
-			anchor: "main",
-			idx: 1
-		}],
-		annotations: {
-			"pl7.app/isAbundance": "true",
-			"pl7.app/abundance/normalized": "false",
-			"pl7.app/abundance/isPrimary": "true"
-		}
-	}]);
-	return [...humanness, ...abundance ?? []].map((c) => ({
-		columnId: c.id,
-		spec: c.spec
-	}));
 }).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title(() => "Humanization Score").subtitle((ctx) => {
 	if (ctx.data.customBlockLabel) return ctx.data.customBlockLabel;
 	return "Humanization Score";
-}).sections((_) => [
-	{
-		type: "link",
-		href: "/",
-		label: "Table"
-	},
-	{
-		type: "link",
-		href: "/histogram",
-		label: "Score Distribution"
-	},
-	{
-		type: "link",
-		href: "/by-sample",
-		label: "By Sample"
-	}
-]).done();
+}).sections((_) => [{
+	type: "link",
+	href: "/",
+	label: "Table"
+}, {
+	type: "link",
+	href: "/histogram",
+	label: "Score Distribution"
+}]).done();
 //#endregion
 exports.HUMANNESS_SCORE_COLUMN = HUMANNESS_SCORE_COLUMN;
-exports.defaultGraphStateBoxplot = defaultGraphStateBoxplot;
 exports.defaultGraphStateHistogram = defaultGraphStateHistogram;
 exports.platforma = platforma;
 

package/dist/index.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.cjs","names":["DataModelBuilder","BlockModelV3","ArrayColumnProvider"],"sources":["../src/index.ts"],"sourcesContent":["import type { GraphMakerState } from '@milaboratories/graph-maker';\nimport type {\n  PColumnIdAndSpec,\n  PFrameHandle,\n  PlDataTableStateV2,\n  PlRef,\n} from '@platforma-sdk/model';\nimport {\n  ArrayColumnProvider,\n  BlockModelV3,\n  DataModelBuilder,\n  createPFrameForGraphs,\n  createPlDataTableStateV2,\n  createPlDataTableV3,\n} from '@platforma-sdk/model';\nexport type * from '@milaboratories/helpers';\n\ntype OldArgs = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n};\n\ntype OldUiState = {\n  tableState: PlDataTableStateV2;\n  graphStateHistogram?: GraphMakerState;\n  graphStateBoxplot?: GraphMakerState;\n};\n\nexport type BlockData = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n  tableState: PlDataTableStateV2;\n  // Distribution of the per-clonotype humanness score across the whole dataset.\n  graphStateHistogram: GraphMakerState;\n  // Per-sample distribution of humanness (box/violin), grouped by sampleId.\n  graphStateBoxplot: GraphMakerState;\n};\n\n// Humanness score column name emitted by `clonotype-process.tpl.tengo`.\nexport const HUMANNESS_SCORE_COLUMN = 'pl7.app/humannessScore';\n\nexport const defaultGraphStateHistogram = (): GraphMakerState => ({\n  title: 'Humanness Score Distribution',\n  template: 'bins',\n  currentTab: null,\n  axesSettings: {\n    other: { binsCount: 20 },\n  },\n});\n\nexport const defaultGraphStateBoxplot = (): GraphMakerState => ({\n  title: 'Humanness by Sample',\n  template: 'box',\n  currentTab: null,\n});\n\n// Selectors for the input dataset anchor — shared between `inputOptions`\n// (the dropdown) and `subtitle` (so the default label matches the dataset name).\nconst inputSelectors = [{\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/clonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}, {\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/scClonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}];\n\nconst dataModel = new DataModelBuilder()\n  .from<BlockData>('v1')\n  .upgradeLegacy<OldArgs, OldUiState>(({ args, uiState }) => ({\n    ...args,\n    tableState: uiState.tableState,\n    graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),\n    graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot(),\n  }))\n  .init(() => ({\n    customBlockLabel: '',\n    tableState: createPlDataTableStateV2(),\n    graphStateHistogram: defaultGraphStateHistogram(),\n    graphStateBoxplot: defaultGraphStateBoxplot(),\n  }));\n\nexport const platforma = BlockModelV3.create(dataModel)\n\n  .args((data) => {\n    if (!data.inputAnchor) throw new Error('Input anchor is required');\n\n    return {\n      // Empty when unset; the workflow falls back to the input dataset name so\n      // the provenance trace label matches the block subtitle.\n      customBlockLabel: data.customBlockLabel || '',\n      inputAnchor: data.inputAnchor,\n      mem: data.mem,\n    };\n  })\n\n  .output('inputOptions', (ctx) =>\n    ctx.resultPool.getOptions(inputSelectors),\n  )\n\n  .outputWithStatus('pt', (ctx) => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n    return createPlDataTableV3(ctx, {\n      tableState: ctx.data.tableState,\n      columns: new ArrayColumnProvider(pCols)\n        .getAllColumns()\n        .map((column) => ({ column, isPrimary: true })),\n    });\n  })\n\n  // --- Score distribution (histogram) ---------------------------------------\n  // One row per clonotype, so the histogram counts UNIQUE clonotypes by humanness\n  // score — it is deliberately NOT weighted by clonotype abundance. The question it\n  // answers is \"how many distinct candidates sit below/above a humanness level\"\n  // (i.e. how much humanization work is there), not \"how human is the repertoire by\n  // read mass\". No human-like threshold line is drawn: this score is a 9-mer\n  // fraction rescaled to 0..100, not a cutoff validated against therapeutic mAbs.\n  .outputWithStatus('histogramPf', (ctx): PFrameHandle | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) return undefined;\n    return createPFrameForGraphs(ctx, pCols);\n  })\n\n  .output('histogramPfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined || pCols.length === 0) return undefined;\n    return pCols.map((c) => ({ columnId: c.id, spec: c.spec }));\n  })\n\n  // --- Per-sample distribution (box / violin) --------------------------------\n  // The humanness column is keyed by clonotypeKey only (sample-agnostic). To get\n  // a per-sample view we join it with the input dataset's primary abundance\n  // column, which carries the [sampleId, clonotypeKey] axes. graph-maker joins on\n  // the shared clonotypeKey axis, so each (sample, clonotype) pair contributes the\n  // clonotype's score — grouping by sampleId then yields a distribution per sample.\n  // This is a box/violin (median + spread + tails) on purpose, not a per-sample\n  // mean: the spread is exactly what a single mean would hide.\n  // Degrades gracefully: if the dataset has no primary-abundance column the join\n  // adds nothing, the sampleId axis is absent, and the page simply can't preselect\n  // a grouping (the chart still opens). VDJ datasets almost always carry abundance.\n  .outputWithStatus('perSamplePf', (ctx): PFrameHandle | undefined => {\n    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (humanness === undefined) return undefined;\n\n    const ref = ctx.data.inputAnchor;\n    if (ref === undefined) return undefined;\n\n    const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{\n      axes: [{ anchor: 'main', idx: 0 }, { anchor: 'main', idx: 1 }],\n      annotations: {\n        'pl7.app/isAbundance': 'true',\n        'pl7.app/abundance/normalized': 'false',\n        'pl7.app/abundance/isPrimary': 'true',\n      },\n    }]);\n\n    return createPFrameForGraphs(ctx, [...humanness, ...(abundance ?? [])]);\n  })\n\n  .output('perSamplePfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (humanness === undefined || humanness.length === 0) return undefined;\n\n    const ref = ctx.data.inputAnchor;\n    if (ref === undefined) return undefined;\n\n    const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{\n      axes: [{ anchor: 'main', idx: 0 }, { anchor: 'main', idx: 1 }],\n      annotations: {\n        'pl7.app/isAbundance': 'true',\n        'pl7.app/abundance/normalized': 'false',\n        'pl7.app/abundance/isPrimary': 'true',\n      },\n    }]);\n\n    return [...humanness, ...(abundance ?? 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+{"version":3,"file":"index.cjs","names":["DataModelBuilder","BlockModelV3"],"sources":["../src/index.ts"],"sourcesContent":["import type { GraphMakerState } from '@milaboratories/graph-maker';\nimport type {\n  PColumnIdAndSpec,\n  PFrameHandle,\n  PlDataTableStateV2,\n  PlRef,\n} from '@platforma-sdk/model';\nimport {\n  BlockModelV3,\n  DataModelBuilder, createPFrameForGraphs,\n  createPlDataTableStateV2,\n  createPlDataTableV3,\n} from '@platforma-sdk/model';\nexport type * from '@milaboratories/helpers';\n\ntype OldArgs = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n};\n\ntype OldUiState = {\n  tableState: PlDataTableStateV2;\n  graphStateHistogram?: GraphMakerState;\n};\n\nexport type BlockData = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n  tableState: PlDataTableStateV2;\n  // Distribution of the per-clonotype humanness score across the whole dataset.\n  graphStateHistogram: GraphMakerState;\n};\n\n// Humanness score column name emitted by `clonotype-process.tpl.tengo`.\nexport const HUMANNESS_SCORE_COLUMN = 'pl7.app/humannessScore';\n\nexport const defaultGraphStateHistogram = (): GraphMakerState => ({\n  title: 'Humanness Score Distribution',\n  template: 'bins',\n  currentTab: null,\n  axesSettings: {\n    other: { binsCount: 20 },\n  },\n  // Give the bars a solid fill instead of the default white — colour values\n  // taken from graph-maker's fixed palette (\"Blue\").\n  layersSettings: {\n    bins: { fillColor: '#2D93FA' },\n  },\n});\n\n// Selectors for the input dataset anchor — shared between `inputOptions`\n// (the dropdown) and `subtitle` (so the default label matches the dataset name).\nconst inputSelectors = [{\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/clonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}, {\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/scClonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}];\n\nconst dataModel = new DataModelBuilder()\n  .from<BlockData>('v1')\n  .upgradeLegacy<OldArgs, OldUiState>(({ args, uiState }) => ({\n    ...args,\n    tableState: uiState.tableState,\n    graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),\n  }))\n  .init(() => ({\n    customBlockLabel: '',\n    tableState: createPlDataTableStateV2(),\n    graphStateHistogram: defaultGraphStateHistogram(),\n  }));\n\nexport const platforma = BlockModelV3.create(dataModel)\n\n  .args((data) => {\n    if (!data.inputAnchor) throw new Error('Input anchor is required');\n\n    return {\n      // Empty when unset; the workflow falls back to the input dataset name so\n      // the provenance trace label matches the block subtitle.\n      customBlockLabel: data.customBlockLabel || '',\n      inputAnchor: data.inputAnchor,\n      mem: data.mem,\n    };\n  })\n\n  .output('inputOptions', (ctx) =>\n    ctx.resultPool.getOptions(inputSelectors),\n  )\n\n  .outputWithStatus('pt', (ctx) => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    const anchorCol = pCols[0];\n    if (anchorCol === undefined) {\n      return undefined;\n    }\n\n    return createPlDataTableV3(ctx, {\n      tableState: ctx.data.tableState,\n      columns: {\n        anchors: { main: anchorCol.spec },\n        selector: { mode: 'enrichment' },\n      },\n    });\n  })\n\n  .outputWithStatus('histogramPf', (ctx): PFrameHandle | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) return undefined;\n    return createPFrameForGraphs(ctx, pCols);\n  })\n\n  .output('histogramPfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined || pCols.length === 0) return undefined;\n    return pCols.map((c) => ({ columnId: c.id, spec: c.spec }));\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Humanization Score')\n\n  .subtitle((ctx) => {\n    if (ctx.data.customBlockLabel) return ctx.data.customBlockLabel;\n    return 'Humanization Score';\n  })\n\n  .sections((_) => [\n    { type: 'link', href: '/', label: 'Table' },\n    { type: 'link', href: '/histogram', label: 'Score Distribution' },\n  ])\n\n  .done();\n"],"mappings":";;;AAoCA,MAAa,yBAAyB;AAEtC,MAAa,oCAAqD;CAChE,OAAO;CACP,UAAU;CACV,YAAY;CACZ,cAAc,EACZ,OAAO,EAAE,WAAW,IAAI,EACzB;CAGD,gBAAgB,EACd,MAAM,EAAE,WAAW,WAAW,EAC/B;CACF;AAID,MAAM,iBAAiB,CAAC;CACtB,MAAM,CACJ,EAAE,MAAM,oBAAoB,EAC5B,EAAE,MAAM,4BAA4B,CACrC;CACD,aAAa,EAAE,oBAAoB,QAAQ;CAC5C,EAAE;CACD,MAAM,CACJ,EAAE,MAAM,oBAAoB,EAC5B,EAAE,MAAM,8BAA8B,CACvC;CACD,aAAa,EAAE,oBAAoB,QAAQ;CAC5C,CAAC;AAEF,MAAM,YAAY,IAAIA,qBAAAA,kBAAkB,CACrC,KAAgB,KAAK,CACrB,eAAoC,EAAE,MAAM,eAAe;CAC1D,GAAG;CACH,YAAY,QAAQ;CACpB,qBAAqB,QAAQ,uBAAuB,4BAA4B;CACjF,EAAE,CACF,YAAY;CACX,kBAAkB;CAClB,aAAA,GAAA,qBAAA,2BAAsC;CACtC,qBAAqB,4BAA4B;CAClD,EAAE;AAEL,MAAa,YAAYC,qBAAAA,aAAa,OAAO,UAAU,CAEpD,MAAM,SAAS;CACd,IAAI,CAAC,KAAK,aAAa,MAAM,IAAI,MAAM,2BAA2B;CAElE,OAAO;EAGL,kBAAkB,KAAK,oBAAoB;EAC3C,aAAa,KAAK;EAClB,KAAK,KAAK;EACX;EACD,CAED,OAAO,iBAAiB,QACvB,IAAI,WAAW,WAAW,eAAe,CAC1C,CAEA,iBAAiB,OAAO,QAAQ;CAC/B,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,GACZ;CAGF,MAAM,YAAY,MAAM;CACxB,IAAI,cAAc,KAAA,GAChB;CAGF,QAAA,GAAA,qBAAA,qBAA2B,KAAK;EAC9B,YAAY,IAAI,KAAK;EACrB,SAAS;GACP,SAAS,EAAE,MAAM,UAAU,MAAM;GACjC,UAAU,EAAE,MAAM,cAAc;GACjC;EACF,CAAC;EACF,CAED,iBAAiB,gBAAgB,QAAkC;CAClE,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,GAAW,OAAO,KAAA;CAChC,QAAA,GAAA,qBAAA,uBAA6B,KAAK,MAAM;EACxC,CAED,OAAO,qBAAqB,QAAwC;CACnE,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,KAAa,MAAM,WAAW,GAAG,OAAO,KAAA;CACtD,OAAO,MAAM,KAAK,OAAO;EAAE,UAAU,EAAE;EAAI,MAAM,EAAE;EAAM,EAAE;EAC3D,CAED,OAAO,cAAc,QAAQ,IAAI,SAAS,mBAAmB,KAAK,MAAM,CAExE,YAAY,qBAAqB,CAEjC,UAAU,QAAQ;CACjB,IAAI,IAAI,KAAK,kBAAkB,OAAO,IAAI,KAAK;CAC/C,OAAO;EACP,CAED,UAAU,MAAM,CACf;CAAE,MAAM;CAAQ,MAAM;CAAK,OAAO;CAAS,EAC3C;CAAE,MAAM;CAAQ,MAAM;CAAc,OAAO;CAAsB,CAClE,CAAC,CAED,MAAM"}

package/dist/index.d.ts

@@ -11,11 +11,9 @@ type BlockData = {
   mem?: number;
   tableState: PlDataTableStateV2;
   graphStateHistogram: GraphMakerState;
-  graphStateBoxplot: GraphMakerState;
 };
 declare const HUMANNESS_SCORE_COLUMN = "pl7.app/humannessScore";
 declare const defaultGraphStateHistogram: () => GraphMakerState;
-declare const defaultGraphStateBoxplot: () => GraphMakerState;
 declare const platforma: _$_platforma_sdk_model0.PlatformaExtended<_$_platforma_sdk_model0.PlatformaV3<BlockData, {
   customBlockLabel: string;
   inputAnchor: Readonly<{
@@ -1722,46 +1720,9 @@ declare const platforma: _$_platforma_sdk_model0.PlatformaExtended<_$_platforma_
       }[];
     };
   }[] | undefined>;
-} & {
-  perSamplePf: _$_platforma_sdk_model0.ConfigRenderLambda<PFrameHandle | undefined> & {
-    withStatus: true;
-  };
-} & {
-  perSamplePfPcols: _$_platforma_sdk_model0.ConfigRenderLambda<{
-    readonly columnId: _$_platforma_sdk_model0.PObjectId;
-    readonly spec: {
-      readonly kind: "PColumn";
-      readonly name: string;
-      readonly domain?: {
-        [x: string]: string;
-      } | undefined;
-      readonly contextDomain?: {
-        [x: string]: string;
-      } | undefined;
-      readonly annotations?: {
-        [x: string]: string;
-      } | undefined;
-      readonly valueType: "Int" | "Long" | "Float" | "Double" | "String" | "Bytes";
-      readonly parentAxes?: number[] | undefined;
-      readonly axesSpec: {
-        readonly type: _$_platforma_sdk_model0.AxisValueType;
-        readonly name: string;
-        readonly domain?: {
-          [x: string]: string;
-        } | undefined;
-        readonly contextDomain?: {
-          [x: string]: string;
-        } | undefined;
-        readonly annotations?: {
-          [x: string]: string;
-        } | undefined;
-        readonly parentAxes?: number[] | undefined;
-      }[];
-    };
-  }[] | undefined>;
 } & {
   isRunning: _$_platforma_sdk_model0.ConfigRenderLambda<boolean>;
-}>, "/" | "/histogram" | "/by-sample", {}, _$_platforma_sdk_model0.BlockDefaultUiServices>>;
+}>, "/" | "/histogram", {}, _$_platforma_sdk_model0.BlockDefaultUiServices>>;
 //#endregion
-export { BlockData, HUMANNESS_SCORE_COLUMN, defaultGraphStateBoxplot, defaultGraphStateHistogram, platforma };
+export { BlockData, HUMANNESS_SCORE_COLUMN, defaultGraphStateHistogram, platforma };
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","names":[],"sources":["../src/index.ts"],"mappings":";;;;;;;KA0BY,SAAA;EACV,gBAAA;EACA,WAAA,GAAc,KAAA;EACd,GAAA;EACA,UAAA,EAAY,kBAAA;EAEZ,mBAAA,EAAqB,eAAA;AAAA;AAAA,cAIV,sBAAA;AAAA,cAEA,0BAAA,QAAiC,eAAA;AAAA,cA2CjC,SAAA,EAAS,uBAAA,CAAA,iBAAA,yBAAA,WAAA,CAAA,SAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;gBAAA"}

package/dist/index.js

@@ -1,16 +1,12 @@
-import { ArrayColumnProvider, BlockModelV3, DataModelBuilder, createPFrameForGraphs, createPlDataTableStateV2, createPlDataTableV3 } from "@platforma-sdk/model";
+import { BlockModelV3, DataModelBuilder, createPFrameForGraphs, createPlDataTableStateV2, createPlDataTableV3 } from "@platforma-sdk/model";
 //#region src/index.ts
 const HUMANNESS_SCORE_COLUMN = "pl7.app/humannessScore";
 const defaultGraphStateHistogram = () => ({
 	title: "Humanness Score Distribution",
 	template: "bins",
 	currentTab: null,
-	axesSettings: { other: { binsCount: 20 } }
-});
-const defaultGraphStateBoxplot = () => ({
-	title: "Humanness by Sample",
-	template: "box",
-	currentTab: null
+	axesSettings: { other: { binsCount: 20 } },
+	layersSettings: { bins: { fillColor: "#2D93FA" } }
 });
 const inputSelectors = [{
 	axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/clonotypeKey" }],
@@ -22,13 +18,11 @@ const inputSelectors = [{
 const dataModel = new DataModelBuilder().from("v1").upgradeLegacy(({ args, uiState }) => ({
 	...args,
 	tableState: uiState.tableState,
-	graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),
-	graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot()
+	graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram()
 })).init(() => ({
 	customBlockLabel: "",
 	tableState: createPlDataTableStateV2(),
-	graphStateHistogram: defaultGraphStateHistogram(),
-	graphStateBoxplot: defaultGraphStateBoxplot()
+	graphStateHistogram: defaultGraphStateHistogram()
 }));
 const platforma = BlockModelV3.create(dataModel).args((data) => {
 	if (!data.inputAnchor) throw new Error("Input anchor is required");
@@ -40,12 +34,14 @@ const platforma = BlockModelV3.create(dataModel).args((data) => {
 }).output("inputOptions", (ctx) => ctx.resultPool.getOptions(inputSelectors)).outputWithStatus("pt", (ctx) => {
 	const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
 	if (pCols === void 0) return;
+	const anchorCol = pCols[0];
+	if (anchorCol === void 0) return;
 	return createPlDataTableV3(ctx, {
 		tableState: ctx.data.tableState,
-		columns: new ArrayColumnProvider(pCols).getAllColumns().map((column) => ({
-			column,
-			isPrimary: true
-		}))
+		columns: {
+			anchors: { main: anchorCol.spec },
+			selector: { mode: "enrichment" }
+		}
 	});
 }).outputWithStatus("histogramPf", (ctx) => {
 	const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
@@ -58,70 +54,19 @@ const platforma = BlockModelV3.create(dataModel).args((data) => {
 		columnId: c.id,
 		spec: c.spec
 	}));
-}).outputWithStatus("perSamplePf", (ctx) => {
-	const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
-	if (humanness === void 0) return void 0;
-	const ref = ctx.data.inputAnchor;
-	if (ref === void 0) return void 0;
-	const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
-		axes: [{
-			anchor: "main",
-			idx: 0
-		}, {
-			anchor: "main",
-			idx: 1
-		}],
-		annotations: {
-			"pl7.app/isAbundance": "true",
-			"pl7.app/abundance/normalized": "false",
-			"pl7.app/abundance/isPrimary": "true"
-		}
-	}]);
-	return createPFrameForGraphs(ctx, [...humanness, ...abundance ?? []]);
-}).output("perSamplePfPcols", (ctx) => {
-	const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
-	if (humanness === void 0 || humanness.length === 0) return void 0;
-	const ref = ctx.data.inputAnchor;
-	if (ref === void 0) return void 0;
-	const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
-		axes: [{
-			anchor: "main",
-			idx: 0
-		}, {
-			anchor: "main",
-			idx: 1
-		}],
-		annotations: {
-			"pl7.app/isAbundance": "true",
-			"pl7.app/abundance/normalized": "false",
-			"pl7.app/abundance/isPrimary": "true"
-		}
-	}]);
-	return [...humanness, ...abundance ?? []].map((c) => ({
-		columnId: c.id,
-		spec: c.spec
-	}));
 }).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title(() => "Humanization Score").subtitle((ctx) => {
 	if (ctx.data.customBlockLabel) return ctx.data.customBlockLabel;
 	return "Humanization Score";
-}).sections((_) => [
-	{
-		type: "link",
-		href: "/",
-		label: "Table"
-	},
-	{
-		type: "link",
-		href: "/histogram",
-		label: "Score Distribution"
-	},
-	{
-		type: "link",
-		href: "/by-sample",
-		label: "By Sample"
-	}
-]).done();
+}).sections((_) => [{
+	type: "link",
+	href: "/",
+	label: "Table"
+}, {
+	type: "link",
+	href: "/histogram",
+	label: "Score Distribution"
+}]).done();
 //#endregion
-export { HUMANNESS_SCORE_COLUMN, defaultGraphStateBoxplot, defaultGraphStateHistogram, platforma };
+export { HUMANNESS_SCORE_COLUMN, defaultGraphStateHistogram, platforma };
 
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","names":[],"sources":["../src/index.ts"],"sourcesContent":["import type { GraphMakerState } from '@milaboratories/graph-maker';\nimport type {\n  PColumnIdAndSpec,\n  PFrameHandle,\n  PlDataTableStateV2,\n  PlRef,\n} from '@platforma-sdk/model';\nimport {\n  ArrayColumnProvider,\n  BlockModelV3,\n  DataModelBuilder,\n  createPFrameForGraphs,\n  createPlDataTableStateV2,\n  createPlDataTableV3,\n} from '@platforma-sdk/model';\nexport type * from '@milaboratories/helpers';\n\ntype OldArgs = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n};\n\ntype OldUiState = {\n  tableState: PlDataTableStateV2;\n  graphStateHistogram?: GraphMakerState;\n  graphStateBoxplot?: GraphMakerState;\n};\n\nexport type BlockData = {\n  customBlockLabel: string;\n  inputAnchor?: PlRef;\n  mem?: number;\n  tableState: PlDataTableStateV2;\n  // Distribution of the per-clonotype humanness score across the whole dataset.\n  graphStateHistogram: GraphMakerState;\n  // Per-sample distribution of humanness (box/violin), grouped by sampleId.\n  graphStateBoxplot: GraphMakerState;\n};\n\n// Humanness score column name emitted by `clonotype-process.tpl.tengo`.\nexport const HUMANNESS_SCORE_COLUMN = 'pl7.app/humannessScore';\n\nexport const defaultGraphStateHistogram = (): GraphMakerState => ({\n  title: 'Humanness Score Distribution',\n  template: 'bins',\n  currentTab: null,\n  axesSettings: {\n    other: { binsCount: 20 },\n  },\n});\n\nexport const defaultGraphStateBoxplot = (): GraphMakerState => ({\n  title: 'Humanness by Sample',\n  template: 'box',\n  currentTab: null,\n});\n\n// Selectors for the input dataset anchor — shared between `inputOptions`\n// (the dropdown) and `subtitle` (so the default label matches the dataset name).\nconst inputSelectors = [{\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/clonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}, {\n  axes: [\n    { name: 'pl7.app/sampleId' },\n    { name: 'pl7.app/vdj/scClonotypeKey' },\n  ],\n  annotations: { 'pl7.app/isAnchor': 'true' },\n}];\n\nconst dataModel = new DataModelBuilder()\n  .from<BlockData>('v1')\n  .upgradeLegacy<OldArgs, OldUiState>(({ args, uiState }) => ({\n    ...args,\n    tableState: uiState.tableState,\n    graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),\n    graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot(),\n  }))\n  .init(() => ({\n    customBlockLabel: '',\n    tableState: createPlDataTableStateV2(),\n    graphStateHistogram: defaultGraphStateHistogram(),\n    graphStateBoxplot: defaultGraphStateBoxplot(),\n  }));\n\nexport const platforma = BlockModelV3.create(dataModel)\n\n  .args((data) => {\n    if (!data.inputAnchor) throw new Error('Input anchor is required');\n\n    return {\n      // Empty when unset; the workflow falls back to the input dataset name so\n      // the provenance trace label matches the block subtitle.\n      customBlockLabel: data.customBlockLabel || '',\n      inputAnchor: data.inputAnchor,\n      mem: data.mem,\n    };\n  })\n\n  .output('inputOptions', (ctx) =>\n    ctx.resultPool.getOptions(inputSelectors),\n  )\n\n  .outputWithStatus('pt', (ctx) => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n    return createPlDataTableV3(ctx, {\n      tableState: ctx.data.tableState,\n      columns: new ArrayColumnProvider(pCols)\n        .getAllColumns()\n        .map((column) => ({ column, isPrimary: true })),\n    });\n  })\n\n  // --- Score distribution (histogram) ---------------------------------------\n  // One row per clonotype, so the histogram counts UNIQUE clonotypes by humanness\n  // score — it is deliberately NOT weighted by clonotype abundance. The question it\n  // answers is \"how many distinct candidates sit below/above a humanness level\"\n  // (i.e. how much humanization work is there), not \"how human is the repertoire by\n  // read mass\". No human-like threshold line is drawn: this score is a 9-mer\n  // fraction rescaled to 0..100, not a cutoff validated against therapeutic mAbs.\n  .outputWithStatus('histogramPf', (ctx): PFrameHandle | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) return undefined;\n    return createPFrameForGraphs(ctx, pCols);\n  })\n\n  .output('histogramPfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined || pCols.length === 0) return undefined;\n    return pCols.map((c) => ({ columnId: c.id, spec: c.spec }));\n  })\n\n  // --- Per-sample distribution (box / violin) --------------------------------\n  // The humanness column is keyed by clonotypeKey only (sample-agnostic). To get\n  // a per-sample view we join it with the input dataset's primary abundance\n  // column, which carries the [sampleId, clonotypeKey] axes. graph-maker joins on\n  // the shared clonotypeKey axis, so each (sample, clonotype) pair contributes the\n  // clonotype's score — grouping by sampleId then yields a distribution per sample.\n  // This is a box/violin (median + spread + tails) on purpose, not a per-sample\n  // mean: the spread is exactly what a single mean would hide.\n  // Degrades gracefully: if the dataset has no primary-abundance column the join\n  // adds nothing, the sampleId axis is absent, and the page simply can't preselect\n  // a grouping (the chart still opens). VDJ datasets almost always carry abundance.\n  .outputWithStatus('perSamplePf', (ctx): PFrameHandle | undefined => {\n    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (humanness === undefined) return undefined;\n\n    const ref = ctx.data.inputAnchor;\n    if (ref === undefined) return undefined;\n\n    const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{\n      axes: [{ anchor: 'main', idx: 0 }, { anchor: 'main', idx: 1 }],\n      annotations: {\n        'pl7.app/isAbundance': 'true',\n        'pl7.app/abundance/normalized': 'false',\n        'pl7.app/abundance/isPrimary': 'true',\n      },\n    }]);\n\n    return createPFrameForGraphs(ctx, [...humanness, ...(abundance ?? [])]);\n  })\n\n  .output('perSamplePfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (humanness === undefined || humanness.length === 0) return undefined;\n\n    const ref = ctx.data.inputAnchor;\n    if (ref === undefined) return undefined;\n\n    const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{\n      axes: [{ anchor: 'main', idx: 0 }, { anchor: 'main', idx: 1 }],\n      annotations: {\n        'pl7.app/isAbundance': 'true',\n        'pl7.app/abundance/normalized': 'false',\n        'pl7.app/abundance/isPrimary': 'true',\n      },\n    }]);\n\n    return [...humanness, ...(abundance ?? 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defaultGraphStateHistogram(),\n  }))\n  .init(() => ({\n    customBlockLabel: '',\n    tableState: createPlDataTableStateV2(),\n    graphStateHistogram: defaultGraphStateHistogram(),\n  }));\n\nexport const platforma = BlockModelV3.create(dataModel)\n\n  .args((data) => {\n    if (!data.inputAnchor) throw new Error('Input anchor is required');\n\n    return {\n      // Empty when unset; the workflow falls back to the input dataset name so\n      // the provenance trace label matches the block subtitle.\n      customBlockLabel: data.customBlockLabel || '',\n      inputAnchor: data.inputAnchor,\n      mem: data.mem,\n    };\n  })\n\n  .output('inputOptions', (ctx) =>\n    ctx.resultPool.getOptions(inputSelectors),\n  )\n\n  .outputWithStatus('pt', (ctx) => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) {\n      return undefined;\n    }\n\n    const anchorCol = pCols[0];\n    if (anchorCol === undefined) {\n      return undefined;\n    }\n\n    return createPlDataTableV3(ctx, {\n      tableState: ctx.data.tableState,\n      columns: {\n        anchors: { main: anchorCol.spec },\n        selector: { mode: 'enrichment' },\n      },\n    });\n  })\n\n  .outputWithStatus('histogramPf', (ctx): PFrameHandle | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined) return undefined;\n    return createPFrameForGraphs(ctx, pCols);\n  })\n\n  .output('histogramPfPcols', (ctx): PColumnIdAndSpec[] | undefined => {\n    const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();\n    if (pCols === undefined || pCols.length === 0) return undefined;\n    return pCols.map((c) => ({ columnId: c.id, spec: c.spec }));\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Humanization Score')\n\n  .subtitle((ctx) => {\n    if (ctx.data.customBlockLabel) return ctx.data.customBlockLabel;\n    return 'Humanization Score';\n  })\n\n  .sections((_) => [\n    { type: 'link', href: '/', label: 'Table' },\n    { type: 'link', href: '/histogram', label: 'Score Distribution' },\n  ])\n\n  .done();\n"],"mappings":";;AAoCA,MAAa,yBAAyB;AAEtC,MAAa,oCAAqD;CAChE,OAAO;CACP,UAAU;CACV,YAAY;CACZ,cAAc,EACZ,OAAO,EAAE,WAAW,IAAI,EACzB;CAGD,gBAAgB,EACd,MAAM,EAAE,WAAW,WAAW,EAC/B;CACF;AAID,MAAM,iBAAiB,CAAC;CACtB,MAAM,CACJ,EAAE,MAAM,oBAAoB,EAC5B,EAAE,MAAM,4BAA4B,CACrC;CACD,aAAa,EAAE,oBAAoB,QAAQ;CAC5C,EAAE;CACD,MAAM,CACJ,EAAE,MAAM,oBAAoB,EAC5B,EAAE,MAAM,8BAA8B,CACvC;CACD,aAAa,EAAE,oBAAoB,QAAQ;CAC5C,CAAC;AAEF,MAAM,YAAY,IAAI,kBAAkB,CACrC,KAAgB,KAAK,CACrB,eAAoC,EAAE,MAAM,eAAe;CAC1D,GAAG;CACH,YAAY,QAAQ;CACpB,qBAAqB,QAAQ,uBAAuB,4BAA4B;CACjF,EAAE,CACF,YAAY;CACX,kBAAkB;CAClB,YAAY,0BAA0B;CACtC,qBAAqB,4BAA4B;CAClD,EAAE;AAEL,MAAa,YAAY,aAAa,OAAO,UAAU,CAEpD,MAAM,SAAS;CACd,IAAI,CAAC,KAAK,aAAa,MAAM,IAAI,MAAM,2BAA2B;CAElE,OAAO;EAGL,kBAAkB,KAAK,oBAAoB;EAC3C,aAAa,KAAK;EAClB,KAAK,KAAK;EACX;EACD,CAED,OAAO,iBAAiB,QACvB,IAAI,WAAW,WAAW,eAAe,CAC1C,CAEA,iBAAiB,OAAO,QAAQ;CAC/B,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,GACZ;CAGF,MAAM,YAAY,MAAM;CACxB,IAAI,cAAc,KAAA,GAChB;CAGF,OAAO,oBAAoB,KAAK;EAC9B,YAAY,IAAI,KAAK;EACrB,SAAS;GACP,SAAS,EAAE,MAAM,UAAU,MAAM;GACjC,UAAU,EAAE,MAAM,cAAc;GACjC;EACF,CAAC;EACF,CAED,iBAAiB,gBAAgB,QAAkC;CAClE,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,GAAW,OAAO,KAAA;CAChC,OAAO,sBAAsB,KAAK,MAAM;EACxC,CAED,OAAO,qBAAqB,QAAwC;CACnE,MAAM,QAAQ,IAAI,SAAS,QAAQ,kBAAkB,EAAE,aAAa;CACpE,IAAI,UAAU,KAAA,KAAa,MAAM,WAAW,GAAG,OAAO,KAAA;CACtD,OAAO,MAAM,KAAK,OAAO;EAAE,UAAU,EAAE;EAAI,MAAM,EAAE;EAAM,EAAE;EAC3D,CAED,OAAO,cAAc,QAAQ,IAAI,SAAS,mBAAmB,KAAK,MAAM,CAExE,YAAY,qBAAqB,CAEjC,UAAU,QAAQ;CACjB,IAAI,IAAI,KAAK,kBAAkB,OAAO,IAAI,KAAK;CAC/C,OAAO;EACP,CAED,UAAU,MAAM,CACf;CAAE,MAAM;CAAQ,MAAM;CAAK,OAAO;CAAS,EAC3C;CAAE,MAAM;CAAQ,MAAM;CAAc,OAAO;CAAsB,CAClE,CAAC,CAED,MAAM"}