@datagrok/peptides 0.8.6 → 0.8.7

package/package.json

@@ -1,13 +1,13 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.8.6",
+	"version": "0.8.7",
 	"description": "",
 	"dependencies": {
 		"@biowasm/aioli": ">=2.4.0",
 		"@datagrok-libraries/bio": ">=0.0.4",
-		"@datagrok-libraries/ml": ">=0.0.10",
+		"@datagrok-libraries/ml": ">=0.0.14",
 		"@datagrok-libraries/statistics": ">=0.1.5",
-		"@datagrok-libraries/utils": ">=0.0.18",
+		"@datagrok-libraries/utils": ">=0.0.22",
 		"@types/d3": "^7.0.0",
 		"@types/jquery": "^3.5.6",
 		"cash-dom": "latest",

package/src/describe.ts

@@ -3,6 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import {splitAlignedPeptides} from './utils/split-aligned';
 import {tTest} from '@datagrok-libraries/statistics/src/tests';
 import {fdrcorrection} from '@datagrok-libraries/statistics/src/multiple-tests';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 import {ChemPalette} from './utils/chem-palette';
 import {setAARRenderer} from './utils/cell-renderer';
 
@@ -132,7 +133,7 @@ async function calculateStatistics(
   activityColumnScaled: string,
   peptidesCount: number,
   splitSeqDf: DG.DataFrame,
-  groupMapping: {[key: string]: string},
+  groupMapping: StringDictionary,
 ) {
   matrixDf = matrixDf.groupBy([positionColName, aminoAcidResidue])
     .add('count', activityColumnScaled, 'Count')
@@ -446,7 +447,7 @@ export async function describe(
   twoColorMode: boolean,
   initialBitset: DG.BitSet | null,
   grouping: boolean,
-): Promise<[DG.Grid, DG.Grid, DG.DataFrame, {[key: string]: string}]> {
+): Promise<[DG.Grid, DG.Grid, DG.DataFrame, StringDictionary]> {
   //Split the aligned sequence into separate AARs
   let splitSeqDf: DG.DataFrame | undefined;
   let invalidIndexes: number[];
@@ -484,7 +485,7 @@ export async function describe(
   let matrixDf = splitSeqDf.unpivot([activityColumnScaled], positionColumns, positionColName, aminoAcidResidue);
 
   //TODO: move to chem palette
-  let groupMapping: {[key: string]: string} = {};
+  let groupMapping: StringDictionary = {};
   if (grouping) {
     groupMapping = aarGroups;
     const aarCol = matrixDf.getCol(aminoAcidResidue);

package/src/model.ts

@@ -2,6 +2,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {describe} from './describe';
 import {Subject} from 'rxjs';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
  * Model class for SAR viewers that retrieves and stores data.
@@ -12,7 +13,7 @@ class SARViewerModel {
   private viewerGrid: Subject<DG.Grid> = new Subject<DG.Grid>();
   private viewerVGrid: Subject<DG.Grid> = new Subject<DG.Grid>();
   private statsDf: Subject<DG.DataFrame> = new Subject<DG.DataFrame>();
-  private groupMapping: Subject<{[key: string]: string}> = new Subject<{[key: string]: string}>();
+  private groupMapping: Subject<StringDictionary> = new Subject<StringDictionary>();
   public viewerGrid$;
   public viewerVGrid$;
   public statsDf$;

package/src/package-test.ts

@@ -4,6 +4,7 @@ import {runTests} from '@datagrok-libraries/utils/src/test';
 
 import './tests/peptide-space-test';
 import './tests/peptides-tests';
+import './tests/msa-tests';
 
 export const _package = new DG.Package();
 

package/src/package.ts

@@ -5,6 +5,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {
   AlignedSequenceCellRenderer,
+  AlignedSequenceDifferenceCellRenderer,
   AminoAcidsCellRenderer,
 } from './utils/cell-renderer';
 import {Logo} from './viewers/logo-viewer';
@@ -17,6 +18,7 @@ import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
 import {peptideMoleculeWidget, getMolecule} from './widgets/peptide-molecule';
 import {SubstViewer} from './viewers/subst-viewer';
 import {runKalign} from './utils/multiple-sequence-alignment';
+import { SemanticValue } from 'datagrok-api/dg';
 
 export const _package = new DG.Package();
 let tableGrid: DG.Grid;
@@ -221,3 +223,33 @@ export async function multipleSequenceAlignment(col: DG.Column): Promise<DG.Data
   table.columns.add(msaCol);
   return table;
 }
+
+//name: Substitution
+//tags: panel, widgets
+//input: dataframe table {semType: Substitution}
+//output: widget result
+export async function peptideSubstitution(table: DG.DataFrame): Promise<DG.Widget> {
+  if (!table) {
+    return new DG.Widget(ui.label('No difference'));
+  }
+  let initialCol: DG.Column = table.columns.byName('Initial');
+  let substitutedCol: DG.Column = table.columns.byName('Substituted');
+
+  for (let i = 0; i < initialCol.length; ++i) {
+    let concat = initialCol.get(i) + '#' + substitutedCol.get(i);
+    initialCol.set(i, concat);
+  }
+
+  initialCol.semType = 'alignedSequenceDifference';
+  initialCol.name = 'Substitution';
+  table.columns.remove('Substituted');
+  return new DG.Widget(ui.divH([table.plot.grid().root]));
+}
+
+//name: alignedSequenceDifferenceCellRenderer
+//tags: cellRenderer, cellRenderer-alignedSequenceDifference
+//meta-cell-renderer-sem-type: alignedSequenceDifference
+//output: grid_cell_renderer result
+export function alignedSequenceDifferenceCellRenderer() {
+  return new AlignedSequenceDifferenceCellRenderer();
+}

package/src/peptides.ts

@@ -3,6 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import {createPeptideSimilaritySpaceViewer} from './utils/peptide-similarity-space';
 import {addViewerToHeader} from './viewers/stacked-barchart-viewer';
 import {model} from './model';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 // import $ from 'cash-dom';
 
 /**
@@ -24,16 +25,15 @@ export class Peptides {
    * @param {DG.Grid} tableGrid Working talbe grid.
    * @param {DG.TableView} view Working view.
    * @param {DG.DataFrame} currentDf Working table.
-   * @param {{[key: string]: string}} options SAR viewer options
+   * @param {StringDictionary} options SAR viewer options
    * @param {DG.Column} col Aligned sequences column.
-   * @param {string} activityColumnChoice Activity column name.
    * @memberof Peptides
    */
   async init(
     tableGrid: DG.Grid,
     view: DG.TableView,
     currentDf: DG.DataFrame,
-    options: {[key: string]: string},
+    options: StringDictionary,
     col: DG.Column,
   ) {
     for (let i = 0; i < tableGrid.columns.length; i++) {
@@ -52,7 +52,7 @@ export class Peptides {
     const originalDfName = currentDf.name;
 
     // const substViewer = view.addViewer(
-    //   'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
+    //   'substitution-analysis-viewer', {'activityColumnName': `${options['activityColumnName']}Scaled`},
     // );
     // const substNode = view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis');
 
@@ -76,11 +76,11 @@ export class Peptides {
       'Levenshtein',
       100,
       view,
-      `${options['activityColumnChoice']}Scaled`,
+      `${options['activityColumnName']}Scaled`,
     );
     const psNode = view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
 
-    const layout2 = view.saveLayout();
+    // const layout2 = view.saveLayout();
 
     const nodeList = [sarNode, sarVNode, psNode];
 
@@ -142,7 +142,7 @@ export class Peptides {
         const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
 
         const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
-          currentDf, col, 't-SNE', 'Levenshtein', 100, view, `${options['activityColumnChoice']}Scaled`);
+          currentDf, col, 't-SNE', 'Levenshtein', 100, view, `${options['activityColumnName']}Scaled`);
         const psNode = view.dockManager.dock(
           peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
 
@@ -154,7 +154,7 @@ export class Peptides {
         $(switchViewers).addClass('fa-toggle-on');
       } else {
         const substViewer = view.addViewer(
-          'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
+          'substitution-analysis-viewer', {'activityColumnName': `${options['activityColumnName']}Scaled`},
         );
         substViewer.helpUrl = helpUrl;
         nodeList.push(view.dockManager.dock(substViewer, DG.DOCK_TYPE.DOWN, null, 'Substitution Analysis'));

package/src/tests/msa-tests.ts

@@ -0,0 +1,27 @@
+import {category, test} from '@datagrok-libraries/utils/src/test';
+import {
+  _testMSAIsCorrect,
+  _testTableIsNotEmpty,
+} from './utils';
+import {aligned1} from './test-data';
+
+import * as DG from 'datagrok-api/dg';
+//import * as grok from 'datagrok-api/grok';
+
+export const _package = new DG.Package();
+
+let table: DG.DataFrame;
+
+category('peptides', async () => {
+  //table = await grok.data.files.openTable('Demo:Files/bio/peptides.csv');
+  table = DG.DataFrame.fromCsv(aligned1);
+  const alignedSequencesColumn = table.getCol('AlignedSequence');
+
+  test('MSA.test_table.is_not_empty', async () => {
+    _testTableIsNotEmpty(table);
+  });
+
+  test('MSA.is_correct', async () => {
+    _testMSAIsCorrect(alignedSequencesColumn);
+  });
+});

package/src/tests/peptide-space-test.ts

@@ -1,21 +1,53 @@
-import {category, test} from '@datagrok-libraries/utils/src/test';
+import {/*before, after, */category, test} from '@datagrok-libraries/utils/src/test';
 import {
   _testViewerIsDrawing,
   _testDimensionalityReducer,
   _testPeptideSimilaritySpaceViewer,
+  _testTableIsNotEmpty,
 } from './utils';
 import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {cleanAlignedSequencesColumn} from '../utils/peptide-similarity-space';
+import {aligned1} from './test-data';
 
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+import { StringMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
 
+export const _package = new DG.Package();
+
+let table: DG.DataFrame;
+let view: DG.TableView;
+
+//const table = await grok.data.loadTable(`${_package.webRoot}files/aligned.csv`);
+//'/home/www/data/dev/packages/data/peptides/aligned.csv');
+//console.log(table);
+//const table = await grok.data.files.openTable('Demo:Files/bio/peptides.csv');
 
 category('peptides', async () => {
-  const table = await grok.data.files.openTable('Demo:TestJobs:Files:DemoFiles/bio/peptides.csv');
-  const view = grok.shell.v as DG.TableView;
+  /*before(async () => {
+    console.log(['before']);
+    // const text = await _package.files.readAsText('aligned.csv');
+    // console.log([text]);
+    // table = DG.DataFrame.fromCsv(text);
+
+    // const path = `${_package.webRoot}files/aligned.csv`;
+    // console.log([path]);
+    // table = await grok.data.loadTable(path);
+    // console.log([table]);
+
+    table = await grok.data.files.openTable('Demo:Files/bio/peptides.csv');
+    view = grok.shell.addTableView(table);
+  });*/
 
-  test('PeptideSimilaritySpaceWidget.is_drawing', async () => {
+  //table = await grok.data.files.openTable('Demo:Files/bio/peptides.csv');
+  table = DG.DataFrame.fromCsv(aligned1);
+  view = grok.shell.addTableView(table);
+
+  test('peptide_space.test_table.is_not_empty', async () => {
+    _testTableIsNotEmpty(table);
+  });
+
+  test('peptide_space.PeptideSimilaritySpaceWidget.is_drawing', async () => {
     await _testViewerIsDrawing(table, view);
   });
 
@@ -23,18 +55,23 @@ category('peptides', async () => {
   const columnData = cleanAlignedSequencesColumn(alignedSequencesColumn);
 
   for (const method of DimensionalityReducer.availableMethods) {
-    for (const measure of DimensionalityReducer.availableMetrics) {
-      test(`DimensinalityReducer.${method}.${measure}.is_numeric`, async () => {
-        await _testDimensionalityReducer(columnData, method, measure);
+    for (const measure of DimensionalityReducer.availableMetricsByType('String')) {
+      test(`peptide_space.DimensinalityReducer.${method}.${measure}.is_numeric`, async () => {
+        await _testDimensionalityReducer(columnData, method as StringMetrics, measure);
       });
     }
   }
 
   for (const method of DimensionalityReducer.availableMethods) {
-    for (const measure of DimensionalityReducer.availableMetrics) {
-      test(`peptides.PeptideSimilaritySpaceViewer.${method}.${measure}.is_proper`, async () => {
+    for (const measure of DimensionalityReducer.availableMetricsByType('String')) {
+      test(`peptide_space.PeptideSimilaritySpaceViewer.${method}.${measure}.is_proper`, async () => {
         await _testPeptideSimilaritySpaceViewer(table, alignedSequencesColumn, method, measure, 100);//, view);
       });
     }
   }
+
+  /*after(async () => {
+    view.close();
+    grok.shell.closeTable(table!);
+  });*/
 });

package/src/tests/peptides-tests.ts

@@ -1,4 +1,5 @@
 import {after, before, category, test} from '@datagrok-libraries/utils/src/test';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 import {splitAlignedPeptides} from '../utils/split-aligned';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
@@ -13,7 +14,7 @@ import * as P from '../package';
 
 category('peptides', async () => {
   let peptidesDf: DG.DataFrame;
-  let options: {[key: string]: string};
+  let options: StringDictionary;
   let peptidesGrid: DG.Grid;
   let asCol: DG.Column;
   let pepView: DG.TableView;