@datagrok/peptides 1.3.0 → 1.3.2

package/src/tests/core.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 import {category, test, expect, delay} from '@datagrok-libraries/utils/src/test';
 
 import {_package} from '../package-test';
-import {startAnalysis} from '../widgets/analyze-peptides';
+import {startAnalysis} from '../widgets/peptides';
 import {PeptidesModel} from '../model';
 import * as C from '../utils/constants';
 import {scaleActivity} from '../utils/misc';
@@ -14,6 +14,7 @@ category('Core', () => {
   let simpleActivityCol: DG.Column<number>;
   let simpleAlignedSeqCol: DG.Column<string>;
   let simpleScaledDf: DG.DataFrame;
+  let scalingFormula: (x: number) => number;
   let simpleScaledColName: string;
 
   let complexTable: DG.DataFrame;
@@ -34,10 +35,10 @@ category('Core', () => {
     simpleAlignedSeqCol.tags[C.TAGS.ALPHABET] = 'PT';
     simpleAlignedSeqCol.tags[DG.TAGS.UNITS] = 'fasta';
     simpleAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
-    [simpleScaledDf, simpleScaledColName] = scaleActivity('-lg', simpleTable, simpleActivityColName, true);
+    [simpleScaledDf, scalingFormula, simpleScaledColName] = scaleActivity('-lg', simpleActivityCol);
 
     model = await startAnalysis(
-      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledDf, simpleScaledColName);
+      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, scalingFormula, simpleScaledColName, '-lg', []);
     expect(model instanceof PeptidesModel, true);
 
     if (model != null) {
@@ -56,10 +57,10 @@ category('Core', () => {
     complexAlignedSeqCol.tags[DG.TAGS.UNITS] = 'separator';
     complexAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
     complexAlignedSeqCol.tags[C.TAGS.SEPARATOR] = '/';
-    [complexScaledDf, complexScaledColName] = scaleActivity('-lg', complexTable, complexActivityColName, true);
+    [complexScaledDf, scalingFormula, complexScaledColName] = scaleActivity('-lg', complexActivityCol);
 
     model = await startAnalysis(
-      complexActivityCol, complexAlignedSeqCol, null, complexTable, complexScaledDf, complexScaledColName);
+      complexActivityCol, complexAlignedSeqCol, null, complexTable, scalingFormula, complexScaledColName, '-lg', []);
     expect(model instanceof PeptidesModel, true);
 
     if (model != null) {
@@ -77,10 +78,10 @@ category('Core', () => {
     simpleAlignedSeqCol.tags[C.TAGS.ALPHABET] = 'PT';
     simpleAlignedSeqCol.tags[DG.TAGS.UNITS] = 'fasta';
     simpleAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
-    [simpleScaledDf, simpleScaledColName] = scaleActivity('-lg', simpleTable, simpleActivityColName, true);
+    [simpleScaledDf, scalingFormula, simpleScaledColName] = scaleActivity('-lg', simpleActivityCol);
 
     model = await startAnalysis(
-      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledDf, simpleScaledColName);
+      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, scalingFormula, simpleScaledColName, '-lg', []);
     let v = grok.shell.getTableView('Peptides analysis');
     const d = v.dataFrame;
     const layout = v.saveLayout();

package/src/utils/cell-renderer.ts

@@ -89,6 +89,18 @@ export function renderInvaraintMapCell(canvasContext: CanvasRenderingContext2D,
     renderCellSelection(canvasContext, bound);
 }
 
+export function renderLogoSummaryCell(canvasContext: CanvasRenderingContext2D, cellValue: number,
+  clusterSelection: number[], bound: DG.Rect): void {
+  canvasContext.font = '13px Roboto, Roboto Local, sans-serif';
+  canvasContext.textAlign = 'center';
+  canvasContext.textBaseline = 'middle';
+  canvasContext.fillStyle = '#000';
+  canvasContext.fillText(cellValue.toString(), bound.x + (bound.width / 2), bound.y + (bound.height / 2), bound.width);
+
+  if (clusterSelection.includes(cellValue))
+    renderCellSelection(canvasContext, bound);
+}
+
 export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, monomerColStats: types.MonomerColStats,
   bounds: DG.Rect, max: number): types.BarCoordinates {
   let sum = col.length - (monomerColStats['-']?.count ?? 0);

package/src/utils/constants.ts

@@ -9,7 +9,8 @@ export enum COLUMNS_NAMES {
   MEAN_DIFFERENCE = 'Mean difference',
   COUNT = 'Count',
   RATIO = 'Ratio',
-  CLUSTERS = '~clusters',
+  CLUSTERS = 'clusters',
+  MACROMOLECULE = 'macromolecule',
 }
 
 export enum CATEGORIES {
@@ -18,13 +19,16 @@ export enum CATEGORIES {
 }
 
 export enum TAGS {
-  AAR = 'AAR',
-  POSITION = 'Pos',
+  MONOMER = 'monomer',
+  POSITION = 'pos',
   SEPARATOR = 'separator',
   SELECTION = 'selection',
   ALPHABET = 'alphabet',
   FILTER = 'filter',
   CLUSTERS = 'clusters',
+  SAR_MODE = 'sarMode',
+  CLUSTER_SELECTION = 'clusterSelection',
+  VISIBLE = 'visible',
 }
 
 export enum SEM_TYPES {

package/src/utils/misc.ts

@@ -32,38 +32,33 @@ export function getSeparator(col: DG.Column<string>): string {
   return col.getTag(C.TAGS.SEPARATOR) ?? '';
 }
 
-export function scaleActivity(
-  activityScaling: string, df: DG.DataFrame, originalActivityName?: string, cloneBitset = false,
-): [DG.DataFrame, string] {
-  let currentActivityColName = originalActivityName ?? C.COLUMNS_NAMES.ACTIVITY;
-  const flag = df.columns.names().includes(currentActivityColName) &&
-    currentActivityColName === originalActivityName;
-  currentActivityColName = flag ? currentActivityColName : C.COLUMNS_NAMES.ACTIVITY;
-  const tempDf = df.clone(cloneBitset ? df.filter : null, [currentActivityColName]);
+export function scaleActivity(activityScaling: string, activityCol: DG.Column<number>, indexes?: number[],
+): [DG.DataFrame, (x: number) => number, string] {
+  const tempDf = DG.DataFrame.create(activityCol.length);
 
-  let formula = (v: number): number => v;
+  let formula = (x: number): number => x;
   let newColName = 'activity';
   switch (activityScaling) {
   case 'none':
     break;
   case 'lg':
-    formula = (v: number): number => Math.log10(v);
+    formula = (x: number): number => Math.log10(x);
     newColName = `Log10(${newColName})`;
     break;
   case '-lg':
-    formula = (v: number): number => -Math.log10(v);
+    formula = (x: number): number => -Math.log10(x);
     newColName = `-Log10(${newColName})`;
     break;
   default:
     throw new Error(`ScalingError: method \`${activityScaling}\` is not available.`);
   }
+  tempDf.columns.addNewVirtual(
+    C.COLUMNS_NAMES.ACTIVITY_SCALED, (i) => {
+      const val = activityCol.get(indexes ? indexes[i] : i);
+      return val ? formula(val) : val;
+    }, DG.TYPE.FLOAT);
 
-  const asCol = tempDf.columns.addNewFloat(C.COLUMNS_NAMES.ACTIVITY_SCALED);
-  const activityCol = df.getCol(currentActivityColName);
-  asCol.init((i) => formula(activityCol.get(i)));
-  df.tags['scaling'] = activityScaling;
-
-  return [tempDf, newColName];
+  return [tempDf, formula, newColName];
 }
 
 export function calculateBarsData(columns: DG.Column<string>[], selection: DG.BitSet): type.MonomerDfStats {

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

@@ -44,7 +44,8 @@ export async function createPeptideSimilaritySpaceViewer(
   const pi = DG.TaskBarProgressIndicator.create('Creating embedding...');
 
   const axesNames = ['~X', '~Y', '~MW'];
-  col ??= table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+  // col ??= table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+  col ??= table.getCol(C.COLUMNS_NAMES.MACROMOLECULE);
   const columnData = col.toList().map((v) => AlignedSequenceEncoder.clean(v));
 
   const reduceDimRes: IReduceDimensionalityResult = await createDimensinalityReducingWorker(

package/src/viewers/logo-summary.ts

@@ -1,12 +1,11 @@
-import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
-import * as C from '../utils/constants';
 import {PeptidesModel} from '../model';
 
 export class LogoSummary extends DG.JsViewer {
+  _titleHost = ui.divText('Logo Summary Table', {id: 'pep-viewer-title'});
   model!: PeptidesModel;
   viewerGrid!: DG.Grid;
   initialized: boolean = false;
@@ -19,7 +18,7 @@ export class LogoSummary extends DG.JsViewer {
     super.onTableAttached();
 
     this.model = await PeptidesModel.getInstance(this.dataFrame);
-    
+
     this.subs.push(this.model.onLogoSummaryGridChanged.subscribe((grid) => {
       this.viewerGrid = grid;
       this.render();
@@ -30,12 +29,13 @@ export class LogoSummary extends DG.JsViewer {
     this.render();
   }
 
-  detach(): void {this.subs.forEach(sub => sub.unsubscribe());}
+  detach(): void {this.subs.forEach((sub) => sub.unsubscribe());}
 
   render(): void {
     if (this.initialized) {
       $(this.root).empty();
-      this.root.appendChild(this.viewerGrid.root);
+      this.viewerGrid.root.style.width = 'auto';
+      this.root.appendChild(ui.divV([this._titleHost, this.viewerGrid.root]));
       this.viewerGrid.invalidate();
     }
   }

package/src/viewers/peptide-space-viewer.ts

@@ -61,8 +61,9 @@ export class PeptideSpaceViewer extends DG.JsViewer {
       this.isEmbeddingCreating = true;
       $(this.root).empty();
       const viewerHost = ui.waitBox(async () => {
-        const aligendSeqCol = this.dataFrame.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
-        const edf = await computeWeights(this.dataFrame, this.method, this.measure, this.cyclesCount, aligendSeqCol);
+        // const aligendSeqCol = this.dataFrame.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+        const alignedSeqCol = this.dataFrame.getCol(C.COLUMNS_NAMES.MACROMOLECULE);
+        const edf = await computeWeights(this.dataFrame, this.method, this.measure, this.cyclesCount, alignedSeqCol);
         this.dataFrame.temp[C.EMBEDDING_STATUS] = true;
         this.model.edf = edf;
 
@@ -92,7 +93,7 @@ export class PeptideSpaceViewer extends DG.JsViewer {
           if (idx != -1) {
             const table = ui.tableFromMap({
               'Activity': colorCol.get(idx),
-              'Sequence': aligendSeqCol.get(idx),
+              'Sequence': alignedSeqCol.get(idx),
               'Row ID': idx,
             });
             ui.tooltip.show(table, ev.clientX, ev.clientY);
@@ -117,7 +118,8 @@ export async function computeWeights(
   let edf: DG.DataFrame | null = null;
   try {
     const axesNames = ['~X', '~Y', '~MW'];
-    col ??= table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+    // col ??= table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+    col ??= table.getCol(C.COLUMNS_NAMES.MACROMOLECULE);
     const columnData = col.toList().map((v) => AlignedSequenceEncoder.clean(v));
 
     const reduceDimRes: IReduceDimensionalityResult = await createDimensinalityReducingWorker(

package/src/viewers/sar-viewer.ts

@@ -21,6 +21,7 @@ export class SARViewerBase extends DG.JsViewer {
   initialized = false;
   isPropertyChanging: boolean = false;
   _isVertical = false;
+  isModeChanging = false;
 
   constructor() {
     super();
@@ -52,20 +53,52 @@ export class SARViewerBase extends DG.JsViewer {
 
   detach(): void {this.subs.forEach((sub) => sub.unsubscribe());}
 
+  get state(): string {
+    return this.dataFrame.getTag(C.TAGS.SAR_MODE) ?? '10';
+  }
+  set state(s: string) {
+    this.dataFrame.setTag(C.TAGS.SAR_MODE, s);
+  }
+
   render(refreshOnly = false): void {
     if (!this.initialized)
       return;
     if (!refreshOnly) {
       $(this.root).empty();
-      const switchHost = ui.div();
+      let switchHost = ui.div();
       if (this.name == 'MC') {
-        const modeSwitch = ui.switchInput('Invariant Map', this.model.isInvariantMap, () => {
-          this.model.isInvariantMap = modeSwitch.value;
-          this._titleHost.innerText = modeSwitch.value ? 'Invariant Map' : 'Mutation Cliffs';
+        const mutationCliffsMode = ui.boolInput('', this.state[0] === '1', () => {
+          if (this.isModeChanging)
+            return;
+          this.isModeChanging = true;
+          invariantMapMode.value = !invariantMapMode.value;
+          this.isModeChanging = false;
+          this._titleHost.innerText = 'Mutation Cliffs';
+          this.model.isInvariantMap = false;
+          this.viewerGrid.invalidate();
+        });
+        mutationCliffsMode.addPostfix('Mutation Cliffs');
+        const invariantMapMode = ui.boolInput('', this.state[1] === '1', () => {
+          if (this.isModeChanging)
+            return;
+          this.isModeChanging = true;
+          mutationCliffsMode.value = !mutationCliffsMode.value;
+          this.isModeChanging = false;
+          this._titleHost.innerText = 'Invariant Map';
+          this.model.isInvariantMap = true;
           this.viewerGrid.invalidate();
         });
-        modeSwitch.root.style.position = 'absolute';
-        switchHost.appendChild(modeSwitch.root);
+        invariantMapMode.addPostfix('Invariant Map');
+        const setDefaultProperties = (input: DG.InputBase): void => {
+          $(input.root).find('.ui-input-editor').css('margin', '0px').attr('type', 'radio');
+          $(input.root).find('.ui-input-description').css('padding', '0px').css('padding-left', '5px');
+        };
+        setDefaultProperties(mutationCliffsMode);
+        setDefaultProperties(invariantMapMode);
+        $(mutationCliffsMode.root).css('padding-right', '10px').css('padding-left', '5px');
+
+        switchHost = ui.divH([mutationCliffsMode.root, invariantMapMode.root]);
+        switchHost.style.position = 'absolute';
       }
       const viewerRoot = this.viewerGrid.root;
       viewerRoot.style.width = 'auto';

package/src/widgets/distribution.ts

@@ -15,6 +15,10 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
   const activityScaledCol = table.columns.bySemType(C.SEM_TYPES.ACTIVITY_SCALED)!;
   const rowCount = activityScaledCol.length;
   const selectionObject = model.mutationCliffsSelection;
+  let isMutationCliffsSelectionEmpty = true;
+  for (const aarList of Object.values(selectionObject))
+    isMutationCliffsSelectionEmpty &&= aarList.length === 0;
+  const clustersObject = model.logoSummarySelection;
   const positions = Object.keys(selectionObject);
   const positionsLen = positions.length;
   let aarStr = allConst;
@@ -29,12 +33,16 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
       otherStr = otherConst;
       for (const position of positions) {
         const posCol = table.getCol(position);
-        for (const aar of selectionObject[position]) {
+        const aarList = selectionObject[position];
+        if (aarList.length === 0)
+          continue;
+
+        for (const aar of aarList) {
           aarStr = `${position} : ${aar}`;
           const splitCol = DG.Column.bool(C.COLUMNS_NAMES.SPLIT_COL, rowCount).init((i) => posCol.get(i) == aar);
 
           const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
-          const currentStatsDf = model.statsDf.rows.match({Pos: position, AAR: aar}).toDataFrame();
+          const currentStatsDf = model.monomerPositionStatsDf.rows.match({Pos: position, AAR: aar}).toDataFrame();
           const stats: Stats = {
             count: currentStatsDf.get(C.COLUMNS_NAMES.COUNT, 0),
             ratio: currentStatsDf.get(C.COLUMNS_NAMES.RATIO, 0),
@@ -49,10 +57,13 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
       }
     } else if (splitByPosition.value) {
       otherStr = otherConst;
-      const activityScaledData = activityScaledCol.getRawData();
+      const activityScaledData = activityScaledCol.toList();
       for (const position of positions) {
         const posCol = table.getCol(position);
         const aarList = selectionObject[position];
+        if (aarList.length === 0)
+          continue;
+
         aarStr = `${position}: {${aarList.join(', ')}}`;
 
         const mask = DG.BitSet.create(rowCount, (i) => aarList.includes(posCol.get(i)));
@@ -80,7 +91,7 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
       }
 
       otherStr = otherConst;
-      const activityScaledData = activityScaledCol.getRawData();
+      const activityScaledData = activityScaledCol.toList();
       for (const aar of aars) {
         const posList = reversedSelectionObject[aar];
         aarStr = `${aar}: {${posList.join(', ')}}`;
@@ -112,14 +123,18 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
           otherStr = otherConst;
         } else if (positionsLen) {
           aarStr = '';
-          for (const position of positions)
-            aarStr += `${position}: {${selectionObject[position].join(', ')}}; `;
-          aarStr = aarStr.slice(0, aarStr.length - 2);
+          for (const position of positions) {
+            const aarList = selectionObject[position];
+            if (aarList.length !== 0)
+              aarStr += `${position}: {${aarList.join(', ')}}; `;
+          }
+          if (clustersObject.length !== 0)
+            aarStr += `Clusters: ${clustersObject.join(', ')}`;
           otherStr = otherConst;
         }
 
         const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
-        const stats = getStats(activityScaledCol.getRawData(), table.selection);
+        const stats = getStats(activityScaledCol.toList(), table.selection);
         const distributionRoot = getDistributionAndStats(distributionTable, stats, aarStr, otherStr);
         $(distributionRoot).addClass('d4-flex-col');
 
@@ -130,9 +145,9 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
   };
 
   const setDefaultProperties = (input: DG.InputBase): void => {
-    input.enabled = positionsLen != 0;
+    input.enabled = !isMutationCliffsSelectionEmpty;
     $(input.root).find('.ui-input-editor').css('margin', '0px');
-    $(input.root).find('.ui-input-description').css('padding', '0px');
+    $(input.root).find('.ui-input-description').css('padding', '0px').css('padding-left', '5px');
   };
 
   const splitByPosition = ui.boolInput('', model.splitByPos, updateDistributionHost);

package/src/widgets/mutation-cliffs.ts

@@ -16,7 +16,8 @@ export function mutationCliffsWidget(table: DG.DataFrame, model: PeptidesModel):
   const substitutionsArray: string[] = [];
   const deltaArray: number[] = [];
   const substitutedToArray: string[] = [];
-  const alignedSeqCol = table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+  // const alignedSeqCol = table.columns.bySemType(C.SEM_TYPES.MACROMOLECULE)!;
+  const alignedSeqCol = table.getCol(C.COLUMNS_NAMES.MACROMOLECULE);
   const activityScaledCol = table.columns.bySemType(C.SEM_TYPES.ACTIVITY_SCALED)!;
   const seenIndexes = new Map<number, number[]>();
 

package/src/widgets/{analyze-peptides.ts → peptides.ts}

@@ -12,10 +12,10 @@ import {scaleActivity} from '../utils/misc';
 
 /** Peptide analysis widget.
  *
- * @param {DG.DataFrame} currentDf Working table
+ * @param {DG.DataFrame} df Working table
  * @param {DG.Column} col Aligned sequence column
  * @return {Promise<DG.Widget>} Widget containing peptide analysis */
-export async function analyzePeptidesWidget(currentDf: DG.DataFrame, col: DG.Column): Promise<DG.Widget> {
+export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): Promise<DG.Widget> {
   if (!col.tags['aligned']?.includes('MSA') && col.tags[DG.TAGS.UNITS].toLowerCase() != 'helm')
     return new DG.Widget(ui.divText('Peptides analysis only works with aligned sequences'));
 
@@ -30,19 +30,27 @@ export async function analyzePeptidesWidget(currentDf: DG.DataFrame, col: DG.Col
   let tempCol = null;
   let scaledDf: DG.DataFrame;
   let newScaledColName: string;
+  let scalingFormula: (x: number) => number;
 
-  for (const column of currentDf.columns.numerical)
+  for (const column of df.columns.numerical)
     tempCol = column.type === DG.TYPE.FLOAT ? column : null;
 
-  const defaultColumn: DG.Column<number> | null = currentDf.col('activity') || currentDf.col('IC50') || tempCol;
+  const defaultActivityColumn: DG.Column<number> | null = df.col('activity') || df.col('IC50') || tempCol;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
+  const indexes: number[] = [];
+  const f = df.filter;
+  df.onFilterChanged.subscribe(() => {
+    for (let i = 0; i < f.length; ++i) {
+      if (f.get(i))
+        indexes.push(i);
+    }
+  });
   const activityScalingMethod = ui.choiceInput(
     'Scaling', 'none', ['none', 'lg', '-lg'],
     async (currentMethod: string): Promise<void> => {
-      const currentActivityCol = activityColumnChoice.value?.name;
-
-      [scaledDf, newScaledColName] = scaleActivity(currentMethod, currentDf, currentActivityCol, true);
+      [scaledDf, scalingFormula, newScaledColName] =
+        scaleActivity(currentMethod, activityColumnChoice.value!, indexes.length !== 0 ? indexes : undefined);
 
       const hist = scaledDf.plot.histogram({
         filteringEnabled: false,
@@ -60,23 +68,23 @@ export async function analyzePeptidesWidget(currentDf: DG.DataFrame, col: DG.Col
 
   const activityScalingMethodState = (_: any): void => {
     activityScalingMethod.enabled = (activityColumnChoice.value ?? false) &&
-      DG.Stats.fromColumn(activityColumnChoice.value!, currentDf.filter).min > 0;
+      DG.Stats.fromColumn(activityColumnChoice.value!, df.filter).min > 0;
     activityScalingMethod.fireChanged();
   };
-  const activityColumnChoice = ui.columnInput('Activity', currentDf, defaultColumn, activityScalingMethodState);
-  const clustersColumnChoice = ui.columnInput('Clusters', currentDf, null);
+  const activityColumnChoice = ui.columnInput('Activity', df, defaultActivityColumn, activityScalingMethodState);
+  const clustersColumnChoice = ui.columnInput('Clusters', df, null);
   activityColumnChoice.fireChanged();
   activityScalingMethod.fireChanged();
 
   const inputsList = [activityColumnChoice, activityScalingMethod, clustersColumnChoice];
 
   const startBtn = ui.button('Launch SAR', async () => {
-    await startAnalysis(
-      activityColumnChoice.value, col, clustersColumnChoice.value, currentDf, scaledDf, newScaledColName);
+    await startAnalysis(activityColumnChoice.value, col, clustersColumnChoice.value, df, scalingFormula,
+      newScaledColName, activityScalingMethod.value ?? 'none', indexes);
   });
   startBtn.style.alignSelf = 'center';
 
-  const viewer = await currentDf.plot.fromType('WebLogo') as WebLogo;
+  const viewer = await df.plot.fromType('WebLogo') as WebLogo;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
@@ -92,26 +100,36 @@ export async function analyzePeptidesWidget(currentDf: DG.DataFrame, col: DG.Col
   );
 }
 
-export async function startAnalysis(
-  activityColumn: DG.Column<number> | null, alignedSeqCol: DG.Column<string>, clustersColumn: DG.Column | null,
-  currentDf: DG.DataFrame, scaledDf: DG.DataFrame, newScaledColName: string): Promise<PeptidesModel | null> {
+export async function startAnalysis(activityColumn: DG.Column<number> | null, peptidesCol: DG.Column<string>,
+  clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaleNum: (x: number) => number, newScaledColName: string,
+  scaling: string, indexes: number[]): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
   if (activityColumn?.type === DG.TYPE.FLOAT) {
-    const activityColumnName: string = activityColumn.name;
-    const cloneColList = [alignedSeqCol.name, activityColumnName];
-    if (clustersColumn)
-      cloneColList.push(clustersColumn.name);
-
+    const f = currentDf.filter;
     //prepare new DF
-    const newDf = currentDf.clone(currentDf.filter, cloneColList);
-    const activityCol = newDf.getCol(activityColumnName);
-    activityCol.name = C.COLUMNS_NAMES.ACTIVITY;
-    activityCol.semType = C.SEM_TYPES.ACTIVITY;
-    newDf.getCol(alignedSeqCol.name).name = C.COLUMNS_NAMES.ALIGNED_SEQUENCE;
-    const activityScaledCol = scaledDf.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
+    const newDf = DG.DataFrame.create(f.trueCount);
+    const getIndex = indexes.length !== 0 ? (i: number) : number => indexes[i] : (i: number): number => i;
+    let activityCol: DG.Column<number> | null = null;
+    for (const col of currentDf.columns.toList()) {
+      let virtualCol: DG.Column<any>;
+      if (col === activityColumn) {
+        virtualCol = newDf.columns.addNewVirtual(
+          C.COLUMNS_NAMES.ACTIVITY, (i) => activityColumn.get(getIndex(i)!), DG.TYPE.FLOAT);
+        activityCol = virtualCol;
+      } else if (col === peptidesCol) {
+        virtualCol = newDf.columns.addNewVirtual(
+          C.COLUMNS_NAMES.MACROMOLECULE, (i) => peptidesCol.get(getIndex(i)!), DG.TYPE.STRING);
+      } else
+        virtualCol = newDf.columns.addNewVirtual(col.name, (i) => col.get(getIndex(i)!), col.type as DG.TYPE);
+      virtualCol.setTag(C.TAGS.VISIBLE, '0');
+    }
+    activityCol!.semType = C.SEM_TYPES.ACTIVITY;
+    const activityScaledCol = newDf.columns.addNewVirtual(C.COLUMNS_NAMES.ACTIVITY_SCALED, (i) => {
+      const val = activityCol!.get(getIndex(i)!);
+      return val ? scaleNum(val) : val;
+    }, DG.TYPE.FLOAT);
     activityScaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
-    newDf.columns.add(activityScaledCol);
     newDf.name = 'Peptides analysis';
     newDf.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newScaledColName;
     if (clustersColumn) {
@@ -119,13 +137,14 @@ export async function startAnalysis(
       newDf.tags[C.TAGS.CLUSTERS] = C.COLUMNS_NAMES.CLUSTERS;
     }
     // newDf.tags[C.PEPTIDES_ANALYSIS] = 'true';
+    newDf.tags['scaling'] = scaling;
 
     let monomerType = 'HELM_AA';
-    if (alignedSeqCol.getTag(DG.TAGS.UNITS).toLowerCase() == 'helm') {
-      const sampleSeq = alignedSeqCol.get(0)!;
+    if (peptidesCol.getTag(DG.TAGS.UNITS).toLowerCase() == 'helm') {
+      const sampleSeq = peptidesCol.get(0)!;
       monomerType = sampleSeq.startsWith('PEPTIDE') ? 'HELM_AA' : 'HELM_BASE';
     } else {
-      const alphabet = alignedSeqCol.tags[C.TAGS.ALPHABET];
+      const alphabet = peptidesCol.tags[C.TAGS.ALPHABET];
       monomerType = alphabet == 'DNA' || alphabet == 'RNA' ? 'HELM_BASE' : 'HELM_AA';
     }
 

package/{test-Peptides-7770371320b2-8cac318e.html → test-Peptides-916a90d7d48b-ea373bf5.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 8cac318e.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit ea373bf5.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,11 +229,14 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 8cac318e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-29 14:06:21</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">118.684s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">101.87s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: TypeError: Cannot read properties of null (reading 'get')
-    at __puppeteer_evaluation_script__:17:71
-    at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/Peptides/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)
-    at ExecutionContext.evaluate (/home/runner/work/public/public/packages/Peptides/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit ea373bf5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-13 13:02:52</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">89.905s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">73.37s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 501 : Peptides.Core.Start analysis: simple : Unable to get project asset "getMonomerLib"
+Test result : Failed : 438 : Peptides.Core.Start analysis: сomplex : Unable to get project asset "getMonomerLib"
+Test result : Failed : 431 : Peptides.Core.Save and load project : Unable to get project asset "getMonomerLib"
+
+    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:40:11
@@ -243,4 +246,31 @@ header {
     at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:30:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div></div></div></div></body></html>
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:66:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
+Test result : Success : 6322 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
+Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
+Test result : Success : 1 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
+Test result : Success : 4207 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
+Test result : Success : 2954 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
+Test result : Success : 3304 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
+Test result : Success : 3696 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 199 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
+Test result : Success : 803 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 166 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
+Test result : Success : 622 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 7452 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
+Test result : Success : 8496 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 2071 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
+Test result : Success : 2746 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
+Test result : Success : 3306 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
+Test result : Success : 4189 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
+Test result : Success : 239 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
+Test result : Success : 732 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 347 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
+Test result : Success : 659 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 7587 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
+Test result : Success : 8158 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
+</pre></div></div></div></div></body></html>