@datagrok/peptides 0.8.13 → 1.0.0

package/src/tests/utils.ts

@@ -4,6 +4,7 @@ import {expect} from '@datagrok-libraries/utils/src/test';
 import {PeptideSimilaritySpaceWidget, createPeptideSimilaritySpaceViewer} from '../utils/peptide-similarity-space';
 import {
   createDimensinalityReducingWorker,
+  IReduceDimensionalityResult,
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {runKalign} from '../utils/multiple-sequence-alignment';
 import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
@@ -13,7 +14,7 @@ import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
  *
  * @param {DG.DataFrame} table Target table.
  */
-export function _testTableIsNotEmpty(table: DG.DataFrame) {
+export function _testTableIsNotEmpty(table: DG.DataFrame): void {
   expect(table.columns.length > 0 && table.rowCount > 0, true);
 }
 
@@ -23,16 +24,9 @@ export function _testTableIsNotEmpty(table: DG.DataFrame) {
  * @param {DG.DataFrame} table Demo table.
  * @param {DG.TableView} view Demo view.
  */
-export async function _testViewerIsDrawing(table: DG.DataFrame, view: DG.TableView) {
-  let noException = true;
-
-  try {
-    const widget = new PeptideSimilaritySpaceWidget(table.getCol('AlignedSequence'), view);
-    await widget.draw();
-  } catch (error) {
-    noException = false;
-  }
-  expect(noException, true);
+export async function _testViewerIsDrawing(table: DG.DataFrame, view: DG.TableView): Promise<void> {
+  const widget = new PeptideSimilaritySpaceWidget(table.getCol('AlignedSequence'), view);
+  await widget.draw();
 }
 
 /**
@@ -42,18 +36,14 @@ export async function _testViewerIsDrawing(table: DG.DataFrame, view: DG.TableVi
  * @param {string} method Embedding method.
  * @param {string} measure Measure to apply to a pair of strings.
  */
-export async function _testDimensionalityReducer(columnData: Array<string>, method: StringMetrics, measure: string) {
-  let noException = true;
+export async function _testDimensionalityReducer(
+  columnData: Array<string>, method: StringMetrics, measure: string): Promise<void> {
   const cyclesCount = 100;
   let embcols;
 
-  try {
-    embcols = await createDimensinalityReducingWorker(
-      {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
-  } catch (error) {
-    noException = false;
-  }
-  expect(noException, true);
+  const reduceDimRes: IReduceDimensionalityResult = await createDimensinalityReducingWorker(
+    {data: columnData, metric: measure as StringMetrics}, method, {cycles: cyclesCount});
+  embcols = reduceDimRes.embedding;
 
   const [X, Y] = embcols as Array<Float32Array>;
 
@@ -73,39 +63,20 @@ export async function _testDimensionalityReducer(columnData: Array<string>, meth
  * @param {(DG.TableView | null)} view Viewer to show graphics on.
  * @param {(string | null)} [activityColumnName] Name of column with activity.
  */
-export async function _testPeptideSimilaritySpaceViewer(
-  table: DG.DataFrame,
-  alignedSequencesColumn: DG.Column,
-  method: string,
-  measure: string,
-  cyclesCount: number,
-) {
-  let noException = true;
+export async function _testPeptideSimilaritySpaceViewer(table: DG.DataFrame, alignedSequencesColumn: DG.Column,
+  method: string, measure: string, cyclesCount: number): Promise<void> {
   let viewer;
   let df: DG.DataFrame;
 
-  try {
-    viewer = await createPeptideSimilaritySpaceViewer(
-      table, method, measure, cyclesCount, undefined, alignedSequencesColumn);
-    df = viewer.dataFrame!;
-  } catch (error) {
-    noException = false;
-  }
-
-  expect(noException, true);
+  viewer = await createPeptideSimilaritySpaceViewer(
+    table, method, measure, cyclesCount, undefined, alignedSequencesColumn);
+  df = viewer.dataFrame;
 
-  noException = true;
+  const axesNames = ['~X', '~Y', '~MW'];
+  const axes = axesNames.map((v) => df.getCol(v).getRawData() as Float32Array);
 
-  try {
-    const axesNames = ['~X', '~Y', '~MW'];
-    const axes = axesNames.map((v) => df?.getCol(v).getRawData() as Float32Array);
-
-    for (const ax of axes)
-      expect(ax.every((v) => v !== null && v !== NaN), true);
-  } catch (error) {
-    noException = false;
-  }
-  expect(noException, true);
+  for (const ax of axes)
+    expect(ax.every((v) => v !== null && v !== NaN), true);
 }
 
 /**
@@ -114,8 +85,7 @@ export async function _testPeptideSimilaritySpaceViewer(
  * @export
  * @param {DG.Column} col Aligned sequences column.
  */
-export async function _testMSAIsCorrect(col: DG.Column) {
+export async function _testMSAIsCorrect(col: DG.Column): Promise<void> {
   const msaCol = await runKalign(col, true);
   expect(msaCol.toList().every((v, i) => v == col.get(i)), true);
 }
-

package/src/utils/cell-renderer.ts

@@ -2,6 +2,7 @@ import {ChemPalette} from './chem-palette';
 import * as DG from 'datagrok-api/dg';
 
 import * as C from './constants';
+import {getSeparator} from './misc';
 
 /**
  * A function to expand column size based on its contents.
@@ -18,7 +19,7 @@ import * as C from './constants';
 export function expandColumn(
   col: DG.Column, grid: DG.Grid, cellRenderSize: (cellVal: string) => number,
   textSizeMult = 10, minSize = 30, maxSize = 650, timeout = 500,
-) {
+): void {
   let maxLen = 0;
   col.categories.forEach((ent: string) => {
     const len = cellRenderSize(ent);
@@ -39,7 +40,7 @@ export function expandColumn(
  * @param {(DG.Grid | null)} [grid=null] Grid that contains the col column.
  * @param {boolean} [grouping=false] Is grouping enabled.
  */
-export function setAARRenderer(col: DG.Column, grid: DG.Grid | null = null, grouping = false) {
+export function setAARRenderer(col: DG.Column, grid: DG.Grid | null = null, grouping = false): void {
   col.semType = C.SEM_TYPES.AMINO_ACIDS;
   col.setTag('cell.renderer', C.SEM_TYPES.AMINO_ACIDS);
   if (grouping)
@@ -48,6 +49,7 @@ export function setAARRenderer(col: DG.Column, grid: DG.Grid | null = null, grou
   if (grid)
     expandColumn(col, grid, (ent) => measureAAR(ent));
 }
+
 /**
  * A function to measure amino acid residue
  *
@@ -81,7 +83,7 @@ function printLeftOrCentered(
   x: number, y: number, w: number, h: number,
   g: CanvasRenderingContext2D, s: string, color = ChemPalette.undefinedColor,
   pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0,
-) {
+): number {
   g.textAlign = 'start';
   let colorPart = pivot == -1 ? s.substring(0) : s.substring(0, pivot);
   if (colorPart.length == 1)
@@ -112,7 +114,7 @@ function printLeftOrCentered(
   const colorTextSize = g.measureText(colorPart);
   const dy = (textSize.fontBoundingBoxAscent + textSize.fontBoundingBoxDescent) / 2;
 
-  function draw(dx1: number, dx2: number) {
+  function draw(dx1: number, dx2: number): void {
     g.fillStyle = color;
     g.globalAlpha = transparencyRate;
     g.fillText(colorPart, x + dx1, y + dy);
@@ -131,59 +133,17 @@ function printLeftOrCentered(
   }
 }
 
-/**
- * Amino acid residue cell renderer.
- *
- * @export
- * @class AminoAcidsCellRenderer
- * @extends {DG.GridCellRenderer}
- */
 export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
   chemPalette: ChemPalette | null;
 
-  /**
-     * Renderer name.
-     *
-     * @readonly
-     * @memberof AminoAcidsCellRenderer
-     */
-  get name() {
-    return 'aminoAcidsCR';
-  }
+  get name(): string {return 'aminoAcidsCR';}
 
-  /**
-     * Cell type.
-     *
-     * @readonly
-     * @memberof AminoAcidsCellRenderer
-     */
-  get cellType() {
-    return C.SEM_TYPES.AMINO_ACIDS;
-  }
+  get cellType(): string {return C.SEM_TYPES.AMINO_ACIDS;}
 
-  /**
-     * Cell height.
-     *
-     * @readonly
-     * @memberof AminoAcidsCellRenderer
-     */
-  get defaultHeight() {
-    return 15;
-  }
+  get defaultHeight(): number {return 15;}
 
-  /**
-     * Cell width.
-     *
-     * @readonly
-     * @memberof AminoAcidsCellRenderer
-     */
-  get defaultWidth() {
-    return 30;
-  }
+  get defaultWidth(): number {return 30;}
 
-  /**
-     * Constructor.
-     */
   constructor() {
     super();
     this.chemPalette = null;
@@ -202,9 +162,7 @@ export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
      */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-    cellStyle: DG.GridCellStyle) {
-    // this.chemPalette ??= new ChemPalette('grok', gridCell.tableColumn?.getTag('groups') ? true : false);
-
+    cellStyle: DG.GridCellStyle): void {
     y -= 2;
     g.save();
     g.beginPath();
@@ -222,53 +180,14 @@ export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
   }
 }
 
-/**
- * Aligned sequence cell renderer.
- *
- * @export
- * @class AlignedSequenceCellRenderer
- * @extends {DG.GridCellRenderer}
- */
 export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
-  /**
-   * Renderer name.
-   *
-   * @readonly
-   * @memberof AlignedSequenceCellRenderer
-   */
-  get name() {
-    return 'alignedSequenceCR';
-  }
+  get name(): string {return 'alignedSequenceCR';}
 
-  /**
-   * Cell type.
-   *
-   * @readonly
-   * @memberof AlignedSequenceCellRenderer
-   */
-  get cellType() {
-    return C.SEM_TYPES.ALIGNED_SEQUENCE;
-  }
+  get cellType(): string {return C.SEM_TYPES.ALIGNED_SEQUENCE;}
 
-  /**
-   * Cell height.
-   *
-   * @readonly
-   * @memberof AlignedSequenceCellRenderer
-   */
-  get defaultHeight() {
-    return 30;
-  }
+  get defaultHeight(): number {return 30;}
 
-  /**
-   * Cell width.
-   *
-   * @readonly
-   * @memberof AlignedSequenceCellRenderer
-   */
-  get defaultWidth() {
-    return 230;
-  }
+  get defaultWidth(): number {return 230;}
 
   /**
    * Cell renderer function.
@@ -285,7 +204,7 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
     cellStyle: DG.GridCellStyle,
-  ) {
+  ): void {
     const grid = gridCell.grid;
     const cell = gridCell.cell;
     w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
@@ -298,7 +217,7 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
     const s: string = cell.value ?? '';
 
     //TODO: can this be replaced/merged with splitSequence?
-    const subParts = s.split('-');
+    const subParts = s.split(getSeparator(cell.column));
     const [text, simplified] = processSequence(subParts);
     const textSize = g.measureText(text.join(''));
     let x1 = Math.max(x, x + (w - textSize.width) / 2);
@@ -317,13 +236,6 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
   }
 }
 
-/**
- * Function for sequence processing.
- *
- * @export
- * @param {string[]} subParts Sequence subparts.
- * @return {[string[], boolean]}
- */
 export function processSequence(subParts: string[]): [string[], boolean] {
   const simplified = !subParts.some((amino, index) =>
     amino.length > 1 &&
@@ -341,53 +253,14 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   return [text, simplified];
 }
 
-/**
- * Aligned sequence difference cell renderer.
- *
- * @export
- * @class AlignedSequenceDifferenceCellRenderer
- * @extends {DG.GridCellRenderer}
- */
 export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
-  /**
-   * Renderer name.
-   *
-   * @readonly
-   * @memberof AlignedSequenceDifferenceCellRenderer
-   */
-  get name() {
-    return 'alignedSequenceDifferenceCR';
-  }
+  get name(): string {return 'alignedSequenceDifferenceCR';}
 
-  /**
-   * Cell type.
-   *
-   * @readonly
-   * @memberof AlignedSequenceDifferenceCellRenderer
-   */
-  get cellType() {
-    return 'alignedSequenceDifference';
-  }
+  get cellType(): string {return C.SEM_TYPES.ALIGNED_SEQUENCE_DIFFERENCE;}
 
-  /**
-   * Cell height.
-   *
-   * @readonly
-   * @memberof AlignedSequenceDifferenceCellRenderer
-   */
-  get defaultHeight() {
-    return 30;
-  }
+  get defaultHeight(): number {return 30;}
 
-  /**
-   * Cell width.
-   *
-   * @readonly
-   * @memberof AlignedSequenceDifferenceCellRenderer
-   */
-  get defaultWidth() {
-    return 230;
-  }
+  get defaultWidth(): number {return 230;}
 
   /**
    * Cell renderer function.
@@ -403,7 +276,7 @@ export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
    */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-    cellStyle: DG.GridCellStyle) {
+    cellStyle: DG.GridCellStyle): void {
     const grid = gridCell.grid;
     const cell = gridCell.cell;
 
@@ -418,8 +291,9 @@ export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
 
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
-    const subParts1 = s1.split('-');
-    const subParts2 = s2.split('-');
+    const separator = getSeparator(gridCell.tableColumn!);
+    const subParts1 = s1.split(separator);
+    const subParts2 = s2.split(separator);
     const [text] = processSequence(subParts1);
     const textSize = g.measureText(text.join(''));
     let updatedX = Math.max(x, x + (w - (textSize.width + subParts1.length * 4)) / 2);

package/src/utils/chem-palette.ts

@@ -31,15 +31,7 @@ export class ChemPalette {
    * @param {number} y y coordinate of the mouse pointer.
    * @param {MonomerLibrary} monomerLib Monomer Library instance
    */
-  static showTooltip(cell: DG.GridCell, x: number, y: number, monomerLib: MonomerLibrary) {
-    // if (!this.isInit) {
-    //   const validPackage = _package ?? _packageTest;
-    //   if (!validPackage)
-    //     throw new Error('No package instance found');
-    //   this.monomerLib = new MonomerLibrary(await validPackage.files.readAsText(`HELMMonomers_June10.sdf`));
-    //   this.isInit = true;
-    // }
-
+  static showTooltip(cell: DG.GridCell, x: number, y: number, monomerLib: MonomerLibrary): void {
     const s = cell.cell.value as string;
     let toDisplay = [ui.divText(s)];
     const [, aarOuter, aarInner] = ChemPalette.getColorAAPivot(s);
@@ -92,7 +84,6 @@ export class ChemPalette {
   }
 
   static getColorAAPivot(monomer: string = '', scheme: 'grok' = 'grok'): [string, string, string, number] {
-    // const chemPaletteInstance = ChemPalette.getDatagrok();
     const chemPaletteInstance = ChemPalette.getPalette(scheme);
     let [outerMonomer, innerMonomer] = ChemPalette.getInnerOuter(monomer);
     outerMonomer = (outerMonomer.length > 6 ? `${outerMonomer.slice(0, 3)}...` : outerMonomer);
@@ -281,11 +272,9 @@ export class ChemPalette {
   }
 
   static getPalette(scheme: 'grok'): StringDictionary {
-    switch (scheme) {
-    case 'grok':
+    if (scheme == 'grok')
       return ChemPalette.getDatagrok();
-    default:
+    else
       throw new Error(`ChemPalette: scheme \`${scheme}\` does not exist`);
-    }
   }
 }

package/src/utils/constants.ts

@@ -17,11 +17,16 @@ export enum CATEGORIES {
 export enum TAGS {
   AAR = 'AAR',
   POSITION = 'Pos',
+  SEPARATOR = 'monomer-separator',
+  SELECTION = 'selection',
 }
 
 export enum SEM_TYPES {
   AMINO_ACIDS = 'aminoAcids',
   ALIGNED_SEQUENCE = 'alignedSequence',
+  ALIGNED_SEQUENCE_DIFFERENCE = 'alignedSequenceDifference',
+  ACTIVITY = 'activity',
+  ACTIVITY_SCALED = 'activityScaled',
 }
 
 export const STATS = 'stats';

package/src/utils/filtering-statistics.ts

@@ -21,13 +21,13 @@ export class FilteringStatistics {
    * Sets values to make statistical analysis.
    * @param {Float32Array} data Those values.
    */
-  setData(data: Float32Array) {this.data = data;}
+  setData(data: Float32Array): void {this.data = data;}
 
   /**
    * Sets bit mask to split population into two groups.
    * @param {DG.BitSet} mask The mask to perform splitting.
    */
-  setMask(mask: DG.BitSet) {
+  setMask(mask: DG.BitSet): void {
     if (!this.data)
       return;
     const selected = this.data.filter((_, i) => mask.get(i));

package/src/utils/misc.ts

@@ -0,0 +1,29 @@
+import * as DG from 'datagrok-api/dg';
+
+import * as C from './constants';
+
+export function stringToBool(str: string): boolean {
+  return str === 'true' ? true : false;
+}
+
+export function getSeparator(col: DG.Column<string>): string {
+  const separator = col.tags[C.TAGS.SEPARATOR];
+  if (separator)
+    return separator as string;
+
+  const defaultSeparators = ['.', '-', ' '];
+  const categories = col.categories;
+  const catLen = categories.length;
+  for (const potentialSeparator of defaultSeparators) {
+    if (categories.filter((sequence) => sequence.includes(potentialSeparator)).length == catLen)
+      return potentialSeparator;
+  }
+  return separator as string ?? '';
+}
+
+export function getTypedArrayConstructor(
+  maxNum: number): Uint8ArrayConstructor | Uint16ArrayConstructor | Uint32ArrayConstructor {
+  return maxNum < 256 ? Uint8Array :
+    maxNum < 65536 ? Uint16Array :
+      Uint32Array;
+}

package/src/utils/multiple-sequence-alignment.ts

@@ -4,10 +4,7 @@ import * as DG from 'datagrok-api/dg';
 import Aioli from '@biowasm/aioli';
 
 import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
-//@ts-ignore
-import {SEMTYPE} from '../semantics';
-
-// let CLI: any = undefined;
+import * as C from './constants';
 
 /**
  * Converts array of sequences into simple fasta string.
@@ -38,10 +35,9 @@ function _fastaToStrings(fasta: string): string[] {
 function _castAligned(seq: string): string {
   let delimited = '';
 
-  for (let i = 0; i < seq.length; ++i) {
-    const char = seq[i];
+  for (const char of seq)
     delimited += char == '-' ? char : `-${char}`;
-  }
+
   return `NH2${delimited}-COOH`;
 }
 
@@ -81,12 +77,6 @@ export async function runKalign(col: DG.Column, isAligned = false) : Promise<DG.
     reinit: true,
   });
 
-  // if (!CLI) {
-  //   CLI = await new Aioli('kalign/3.3.1');
-  //   console.info('kalign CLI was first initialized.');
-  // } else
-  //   console.info('Initialized kalign CLI was reused.');
-
   console.log(['fasta.length =', fasta.length]);
 
   await CLI.fs.writeFile('input.fa', fasta);
@@ -95,16 +85,13 @@ export async function runKalign(col: DG.Column, isAligned = false) : Promise<DG.
 
   console.warn(output);
 
-  // if (!buf)
-  //   console.warn(buf);
-
   const aligned = _fastaToStrings(buf).slice(0, sequences.length);
   const alignedCol = DG.Column.fromStrings(`(${col.name})msa`, _stringsToAligned(aligned));
-  alignedCol.semType = SEMTYPE.ALIGNED;
+  alignedCol.semType = C.SEM_TYPES.ALIGNED_SEQUENCE;
   return alignedCol;
 }
 
-export async function testMSAEnoughMemory(col: DG.Column) {
+export async function testMSAEnoughMemory(col: DG.Column): Promise<void> {
   const sequencesCount = col.length;
   const delta = sequencesCount/100;
 

package/src/utils/multivariate-analysis.ts

@@ -6,21 +6,19 @@ import * as C from './constants';
 import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
 
 export async function callMVA(
-  tableGrid: DG.Grid,
-  view: DG.View,
   currentDf: DG.DataFrame,
   options: {[name: string]: string},
   sequencesCol: DG.Column,
-) {
+): Promise<void> {
   const activityCol = await _scaleColumn(currentDf.getCol(options['activityColumnName']), options['scaling']);
   const encDf = _encodeSequences(sequencesCol);
-  // const scaledColName = `${options['activityColumnName']}scaled`;
 
+  //TODO: is it correct? Is it needed?
   _insertColumns(
     currentDf,
     [DG.Column.fromList('double', C.COLUMNS_NAMES.ACTIVITY_SCALED, activityCol.toList())],
   );
-  _insertColumns(currentDf, encDf.columns);
+  _insertColumns(currentDf, encDf.columns.toList());
 
   const res = await grok.functions.call('MultivariateAnalysis', {
     table: currentDf,
@@ -50,10 +48,9 @@ function _encodeSequences(sequencesCol: DG.Column): DG.DataFrame {
     for (let i = 0; i < nCols; ++i)
       positions[i][j] = enc.encodeLettter(s[i]);
   }
-  const df = DG.DataFrame.fromColumns(positions.map(
+  return DG.DataFrame.fromColumns(positions.map(
     (v, i) => DG.Column.fromFloat32Array((i+1).toString(), v),
   ));
-  return df;
 }
 
 async function _scaleColumn(column: DG.Column, method: string): Promise<DG.Column> {
@@ -67,7 +64,7 @@ async function _scaleColumn(column: DG.Column, method: string): Promise<DG.Colum
   if (newCol == null)
     throw new Error('Column formula returned unexpected null.');
 
-  return newCol!;
+  return newCol;
 }
 
 function _insertColumns(targetDf: DG.DataFrame, columns: DG.Column[]): DG.DataFrame {

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

@@ -7,6 +7,7 @@ import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encod
 import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {
   createDimensinalityReducingWorker,
+  IReduceDimensionalityResult,
 } 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';
@@ -43,16 +44,17 @@ export async function createPeptideSimilaritySpaceViewer(
   const pi = DG.TaskBarProgressIndicator.create('Creating embedding...');
 
   const axesNames = ['~X', '~Y', '~MW'];
-  const columnData = (col ?? table.getCol(C.COLUMNS_NAMES.ALIGNED_SEQUENCE)).toList()
-    .map((v) => AlignedSequenceEncoder.clean(v));
+  col ??= table.columns.bySemType(C.SEM_TYPES.ALIGNED_SEQUENCE)!;
+  const columnData = col.toList().map((v) => AlignedSequenceEncoder.clean(v));
 
-  const embcols = await createDimensinalityReducingWorker(
-    {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+  const reduceDimRes: IReduceDimensionalityResult = await createDimensinalityReducingWorker(
+    {data: columnData, metric: measure as StringMetrics}, method, {cycles: cyclesCount});
 
+  const embcols = reduceDimRes.embedding;
   const columns = Array.from(
     embcols as Coordinates, (v: Float32Array, k) => DG.Column.fromFloat32Array(axesNames[k], v));
 
-  function _getMW(sequences: string[]) {
+  function _getMW(sequences: string[]): Float32Array {
     const mw: Float32Array = new Float32Array(sequences.length);
 
     mw.map((_, index) => getSequenceMolecularWeight(sequences[index] ?? ''));
@@ -66,10 +68,10 @@ export async function createPeptideSimilaritySpaceViewer(
 
   // Add new axes.
   for (const axis of axesNames) {
-    const col = table.col(axis);
+    const axisCol = table.col(axis);
     const newCol = edf.getCol(axis);
 
-    if (col != null) {
+    if (axisCol != null) {
       for (let i = 0; i < newCol.length; ++i) {
         const v = newCol.get(i);
         table.set(axis, i, v);
@@ -78,8 +80,9 @@ export async function createPeptideSimilaritySpaceViewer(
       table.columns.insert(newCol);
   }
 
+  const colorColName = table.columns.bySemType(C.SEM_TYPES.ACTIVITY)?.name ?? '~MW';
   const viewerOptions = {
-    x: '~X', y: '~Y', color: C.COLUMNS_NAMES.ACTIVITY ?? '~MW', size: '~MW', title: 'Peptide Space',
+    x: '~X', y: '~Y', color: colorColName, size: '~MW', title: 'Peptide Space',
     showYSelector: false, showXSelector: false, showColorSelector: false, showSizeSelector: false,
   };
   const viewer = table.plot.scatter(viewerOptions);
@@ -144,7 +147,7 @@ export class PeptideSimilaritySpaceWidget {
    * @protected
    * @memberof PeptideSimilaritySpaceWidget
    */
-  protected async updateViewer() {
+  protected async updateViewer(): Promise<void> {
     const viewer = await this.drawViewer();
     this.viewer.lastChild?.remove();
     this.viewer.appendChild(viewer.root);