@datagrok/peptides 1.7.2 → 1.8.0

package/src/package.ts

@@ -7,23 +7,36 @@ import {analyzePeptidesUI} from './widgets/peptides';
 import {PeptideSimilaritySpaceWidget} from './utils/peptide-similarity-space';
 import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {MonomerPosition, MostPotentResiduesViewer} from './viewers/sar-viewer';
-
+import {getTreeHelper, ITreeHelper} from '@datagrok-libraries/bio/src/trees/tree-helper';
+import {IDendrogramService, getDendrogramService} from '@datagrok-libraries/bio/src/trees/dendrogram';
 import {PeptideSpaceViewer} from './viewers/peptide-space-viewer';
-import {LogoSummary} from './viewers/logo-summary';
+import {LogoSummaryTable} from './viewers/logo-summary';
 import {MonomerWorks} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 import {PeptidesModel} from './model';
 
 let monomerWorks: MonomerWorks | null = null;
+let treeHelper: ITreeHelper | null = null;
+let dendrogramService: IDendrogramService | null = null;
 
 export const _package = new DG.Package();
 
-export function getMonomerWorks(): MonomerWorks | null {
-  return monomerWorks;
+export function getMonomerWorksInstance(): MonomerWorks {
+  return monomerWorks!;
+}
+
+export function getTreeHelperInstance(): ITreeHelper {
+  return treeHelper!;
+}
+
+export function getDendrogramServiceInstance(): IDendrogramService {
+  return dendrogramService!;
 }
 
 //tags: init
 export async function initPeptides(): Promise<void> {
   monomerWorks ??= new MonomerWorks(await grok.functions.call('Bio:getBioLib'));
+  treeHelper ??= await getTreeHelper();
+  dendrogramService ??= await getDendrogramService();
 }
 
 async function openDemoData(chosenFile: string): Promise<void> {
@@ -44,24 +57,22 @@ export function Peptides(): void {
   const wikiLink = ui.link('wiki', 'https://github.com/datagrok-ai/public/blob/master/help/domains/bio/peptides.md');
   const textLink = ui.inlineText(['For more details, see our ', wikiLink, '.']);
 
-  const appDescription = ui.info(
-    [
-      ui.list([
-        '- automatic recognition of peptide sequences',
-        '- native integration with tons of Datagrok out-of-the box features (visualization, filtering, clustering, ' +
+  const appDescription = ui.info([
+    ui.list([
+      '- automatic recognition of peptide sequences',
+      '- native integration with tons of Datagrok out-of-the box features (visualization, filtering, clustering, ' +
         'multivariate analysis, etc)',
-        '- custom rendering in the spreadsheet',
-        '- interactive logo plots',
-        '- rendering residues',
-        '- structure-activity relationship:',
-        ' ',
-        'a) highlighting statistically significant changes in activity in the [position, monomer] spreadsheet',
-        'b) for the specific [position, monomer], visualizing changes of activity distribution (specific monomer in ' +
+      '- custom rendering in the spreadsheet',
+      '- interactive logo plots',
+      '- rendering residues',
+      '- structure-activity relationship:',
+      ' ',
+      'a) highlighting statistically significant changes in activity in the [position, monomer] spreadsheet',
+      'b) for the specific [position, monomer], visualizing changes of activity distribution (specific monomer in ' +
         'this position vs rest of the monomers in this position)',
-        'c) interactivity',
-      ]),
-    ],
-    'Use and analyse peptide sequence data to support your research:',
+      'c) interactivity',
+    ]),
+  ], 'Use and analyse peptide sequence data to support your research:',
   );
 
   const windows = grok.shell.windows;
@@ -101,32 +112,36 @@ export function peptidesPanel(col: DG.Column): DG.Widget {
   return new DG.Widget(analyzeObject.host);
 }
 
-//name: peptide-sar-viewer
-//description: Peptides SAR Viewer
+//name: Monomer-Position
+//description: Peptides Monomer-Position Viewer
 //tags: viewer
+//meta.icon: files/icons/peptide-sar-viewer.svg
 //output: viewer result
-export function sar(): MonomerPosition {
+export function monomerPosition(): MonomerPosition {
   return new MonomerPosition();
 }
 
-//name: peptide-sar-viewer-vertical
-//description: Peptides Vertical SAR Viewer
+//name: Most Potent Residues
+//description: Peptides Most Potent Residues Viewer
 //tags: viewer
+//meta.icon: files/icons/peptide-sar-vertical-viewer.svg
 //output: viewer result
-export function sarVertical(): MostPotentResiduesViewer {
+export function mostPotentResidues(): MostPotentResiduesViewer {
   return new MostPotentResiduesViewer();
 }
 
-//name: logo-summary-viewer
+//name: Logo Summary Table
 //tags: viewer
+//meta.icon: files/icons/logo-summary-viewer.svg
 //output: viewer result
-export function logoSummary(): LogoSummary {
-  return new LogoSummary();
+export function logoSummaryTable(): LogoSummaryTable {
+  return new LogoSummaryTable();
 }
 
 //name: peptide-space-viewer
 //description: Peptide Space Viewer
 //tags: viewer
+//meta.icon: files/icons/peptide-space-viewer.svg
 //output: viewer result
 export function peptideSpace(): PeptideSpaceViewer {
   return new PeptideSpaceViewer();

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

@@ -1,4 +1,4 @@
-import {/*before, after, */after, category, test} from '@datagrok-libraries/utils/src/test';
+import {category, test} from '@datagrok-libraries/utils/src/test';
 import * as utils from './utils';
 import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {cleanAlignedSequencesColumn} from '../utils/peptide-similarity-space';
@@ -7,7 +7,6 @@ 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';
-import {_package} from '../package-test';
 
 let table: DG.DataFrame;
 let view: DG.TableView;

package/src/tests/viewers.ts

@@ -1,6 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import * as grok from 'datagrok-api/grok';
-//import * as ui from 'datagrok-api/ui';
 
 import {category, test, testViewer} from '@datagrok-libraries/utils/src/test';
 import {aligned1} from './test-data';

package/src/utils/cell-renderer.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 
 import * as C from './constants';
 import * as types from './types';
-import {PositionStats, SummaryStats, MonomerPositionStats} from '../model';
+import {PositionStats, MonomerPositionStats} from '../model';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 

package/src/utils/distance-matrix.worker.ts

@@ -0,0 +1,16 @@
+import {DistanceMatrix} from '@datagrok-libraries/bio/src/trees/distance-matrix';
+import {stringDistanceMetricsMethods} from '@datagrok-libraries/ml/src/typed-metrics';
+
+const ctx: Worker = self as any;
+
+ctx.addEventListener('message', async ({data: {peptidesList, metric}}) => {
+  const data: {error?: any, distances?: Float32Array} = {};
+  try {
+    const dm = DistanceMatrix.calc(peptidesList,
+      (a: string, b: string) => stringDistanceMetricsMethods[metric](a, b));
+    data.distances = dm.data;
+  } catch (e) {
+    data.error = e;
+  }
+  self.postMessage(data);
+});

package/src/utils/peptide-similarity-space.ts

@@ -11,7 +11,6 @@ import {
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {Measure, StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
-import * as C from './constants';
 
 /**
  * Cast an aligned sequences column to clean sequences.

package/src/utils/statistics.ts

@@ -1,3 +1,4 @@
+import * as DG from 'datagrok-api/dg';
 import {tTest} from '@datagrok-libraries/statistics/src/tests';
 import {RawData} from './types';
 
@@ -36,3 +37,11 @@ export function getStats(data: RawData | number[], maskInfo: MaskInfo): Stats {
     ratio: selected.length / data.length,
   };
 }
+
+export function getAggregatedValue(col: DG.Column<number>, agg: DG.AggregationType, mask?: DG.BitSet): number {
+  const stat = DG.Stats.fromColumn(col, mask);
+  if (!(agg in stat))
+    throw new Error(`Aggregation type ${agg} is not supported`);
+  //@ts-ignore: this is a hack to avoid using switch to access the getters
+  return stat[agg] as number;
+}

package/src/utils/types.ts

@@ -17,9 +17,13 @@ export type PeptidesSettings = {
   clustersColumnName?: string,
   scaling?: ScalingMethods,
   isBidirectional?: boolean,
+  showMonomerPosition?: boolean,
+  showMostPotentResidues?: boolean,
+  showLogoSummaryTable?: boolean,
+  showDendrogram?: boolean,
   maxMutations?: number,
   minActivityDelta?: number,
-  columns?: {[col: string]: string},
+  columns?: {[col: string]: DG.AggregationType},
 };
 
 export type DrawOptions = {

package/src/utils/worker-creator.ts

@@ -0,0 +1,11 @@
+import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
+
+export function createDistanceMatrixWorker(peptidesList: string[], metric: StringMetrics): Promise<Float32Array> {
+  return new Promise(function(resolve, reject) {
+    const worker = new Worker(new URL('./distance-matrix.worker', import.meta.url));
+    worker.postMessage({peptidesList, metric});
+    worker.onmessage = ({data: {error, distances}}): void => {
+      error ? reject(error) : resolve(distances);
+    };
+  });
+}