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

package/package.json

@@ -1,19 +1,19 @@
 {
   "name": "@platforma-open/milaboratories.humanization-score.model",
-  "version": "0.3.0",
+  "version": "0.3.2",
   "description": "Block model",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "dependencies": {
-    "@platforma-sdk/model": "1.77.15",
+    "@platforma-sdk/model": "1.77.17",
     "@milaboratories/helpers": "1.14.2",
-    "@milaboratories/graph-maker": "1.4.3"
+    "@milaboratories/graph-maker": "1.4.4"
   },
   "devDependencies": {
     "@milaboratories/ts-builder": "1.5.0",
     "@milaboratories/ts-configs": "1.2.3",
-    "@platforma-sdk/block-tools": "2.9.3",
+    "@platforma-sdk/block-tools": "2.10.0",
     "@platforma-sdk/eslint-config": "1.2.0",
     "eslint": "^9.25.1",
     "vitest": "^4.0.7",

package/src/index.ts

@@ -6,10 +6,8 @@ import type {
   PlRef,
 } from '@platforma-sdk/model';
 import {
-  ArrayColumnProvider,
   BlockModelV3,
-  DataModelBuilder,
-  createPFrameForGraphs,
+  DataModelBuilder, createPFrameForGraphs,
   createPlDataTableStateV2,
   createPlDataTableV3,
 } from '@platforma-sdk/model';
@@ -24,7 +22,6 @@ type OldArgs = {
 type OldUiState = {
   tableState: PlDataTableStateV2;
   graphStateHistogram?: GraphMakerState;
-  graphStateBoxplot?: GraphMakerState;
 };
 
 export type BlockData = {
@@ -34,8 +31,6 @@ export type BlockData = {
   tableState: PlDataTableStateV2;
   // Distribution of the per-clonotype humanness score across the whole dataset.
   graphStateHistogram: GraphMakerState;
-  // Per-sample distribution of humanness (box/violin), grouped by sampleId.
-  graphStateBoxplot: GraphMakerState;
 };
 
 // Humanness score column name emitted by `clonotype-process.tpl.tengo`.
@@ -48,12 +43,11 @@ export const defaultGraphStateHistogram = (): GraphMakerState => ({
   axesSettings: {
     other: { binsCount: 20 },
   },
-});
-
-export const defaultGraphStateBoxplot = (): GraphMakerState => ({
-  title: 'Humanness by Sample',
-  template: 'box',
-  currentTab: null,
+  // Give the bars a solid fill instead of the default white — colour values
+  // taken from graph-maker's fixed palette ("Blue").
+  layersSettings: {
+    bins: { fillColor: '#2D93FA' },
+  },
 });
 
 // Selectors for the input dataset anchor — shared between `inputOptions`
@@ -78,13 +72,11 @@ const dataModel = new DataModelBuilder()
     ...args,
     tableState: uiState.tableState,
     graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),
-    graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot(),
   }))
   .init(() => ({
     customBlockLabel: '',
     tableState: createPlDataTableStateV2(),
     graphStateHistogram: defaultGraphStateHistogram(),
-    graphStateBoxplot: defaultGraphStateBoxplot(),
   }));
 
 export const platforma = BlockModelV3.create(dataModel)
@@ -110,21 +102,21 @@ export const platforma = BlockModelV3.create(dataModel)
     if (pCols === undefined) {
       return undefined;
     }
+
+    const anchorCol = pCols[0];
+    if (anchorCol === undefined) {
+      return undefined;
+    }
+
     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' },
+      },
     });
   })
 
-  // --- Score distribution (histogram) ---------------------------------------
-  // One row per clonotype, so the histogram counts UNIQUE clonotypes by humanness
-  // score — it is deliberately NOT weighted by clonotype abundance. The question it
-  // answers is "how many distinct candidates sit below/above a humanness level"
-  // (i.e. how much humanization work is there), not "how human is the repertoire by
-  // read mass". No human-like threshold line is drawn: this score is a 9-mer
-  // fraction rescaled to 0..100, not a cutoff validated against therapeutic mAbs.
   .outputWithStatus('histogramPf', (ctx): PFrameHandle | undefined => {
     const pCols = ctx.outputs?.resolve('outputHumanness')?.getPColumns();
     if (pCols === undefined) return undefined;
@@ -137,55 +129,6 @@ export const platforma = BlockModelV3.create(dataModel)
     return pCols.map((c) => ({ columnId: c.id, spec: c.spec }));
   })
 
-  // --- Per-sample distribution (box / violin) --------------------------------
-  // The humanness column is keyed by clonotypeKey only (sample-agnostic). To get
-  // a per-sample view we join it with the input dataset's primary abundance
-  // column, which carries the [sampleId, clonotypeKey] axes. graph-maker joins on
-  // the shared clonotypeKey axis, so each (sample, clonotype) pair contributes the
-  // clonotype's score — grouping by sampleId then yields a distribution per sample.
-  // This is a box/violin (median + spread + tails) on purpose, not a per-sample
-  // mean: the spread is exactly what a single mean would hide.
-  // Degrades gracefully: if the dataset has no primary-abundance column the join
-  // adds nothing, the sampleId axis is absent, and the page simply can't preselect
-  // a grouping (the chart still opens). VDJ datasets almost always carry abundance.
-  .outputWithStatus('perSamplePf', (ctx): PFrameHandle | undefined => {
-    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();
-    if (humanness === undefined) return undefined;
-
-    const ref = ctx.data.inputAnchor;
-    if (ref === undefined) return undefined;
-
-    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): PColumnIdAndSpec[] | undefined => {
-    const humanness = ctx.outputs?.resolve('outputHumanness')?.getPColumns();
-    if (humanness === undefined || humanness.length === 0) return undefined;
-
-    const ref = ctx.data.inputAnchor;
-    if (ref === undefined) return undefined;
-
-    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')
@@ -198,7 +141,6 @@ export const platforma = BlockModelV3.create(dataModel)
   .sections((_) => [
     { type: 'link', href: '/', label: 'Table' },
     { type: 'link', href: '/histogram', label: 'Score Distribution' },
-    { type: 'link', href: '/by-sample', label: 'By Sample' },
   ])
 
   .done();