@datagrok/peptides 0.4.3 → 0.5.6

package/src/utils/correlation-analysis.ts

@@ -2,8 +2,8 @@
 import * as DG from 'datagrok-api/dg';
 
 import {AlignedSequenceEncoder} from '@datagrok-libraries/utils/src/sequence-encoder';
-import {assert, transposeMatrix} from '@datagrok-libraries/utils/src/operations';
-import {Vector, Matrix} from '@datagrok-libraries/utils/src/type-declarations';
+import {assert} from '@datagrok-libraries/utils/src/operations';
+import {Matrix} from '@datagrok-libraries/utils/src/type-declarations';
 import {kendallsTau} from '@datagrok-libraries/statistics/src/correlation-coefficient';
 
 /**
@@ -13,111 +13,192 @@ import {kendallsTau} from '@datagrok-libraries/statistics/src/correlation-coeffi
  * @param {Matrix} matrix A matrix.
  * @return {DG.DataFrame} The data frame.
  */
-export function matrix2DataFrame(matrix: Matrix): DG.DataFrame {
+function matrix2DataFrame(matrix: Matrix): DG.DataFrame {
   return DG.DataFrame.fromColumns(matrix.map((v, i) => DG.Column.fromFloat32Array(`${i+1}`, v)));
 }
 
 /**
- * Encodes amino acid sequences into a numeric representation.
+ * Encodes sequence into a certain scale.
  *
- * @param {DG.Column} col A column containing the sequences.
- * @return {DG.DataFrame} The resulting data frame.
+ * @param {DG.DataFrame} df A data frame containing the sequences.
+ * @param {string[]} [positionColumns] If given instructs which columns to consider as sequences containing.
+ * @return {DG.DataFrame} The data frame with seqences encoded.
  */
-function calcPositions(col: DG.Column): DG.DataFrame {
-  const sequences = col.toList().map((v, _) => AlignedSequenceEncoder.clean(v));
-  const enc = new AlignedSequenceEncoder();
-  const encSeqs = sequences.map((v) => Vector.from(enc.encode(v)));
-  const positions = transposeMatrix(encSeqs);
-  return matrix2DataFrame(positions);
+function encodeSequences(df: DG.DataFrame, positionColumns?: string[]): DG.DataFrame {
+  const [nCols, nRows] = [positionColumns ? positionColumns.length : df.columns.length, df.rowCount];
+  const enc = new AlignedSequenceEncoder('WimleyWhite');
+  const positions = new Array(nCols).fill(0).map((_) => new Float32Array(nRows));
+
+  for (let i = 0; i < nCols; ++i) {
+    const col: DG.Column = positionColumns ? df.getCol(positionColumns[i]) : df.columns.byIndex(i);
+
+    for (let j = 0; j < nRows; ++j) {
+      const letter = col.get(j);
+      positions[i][j] = enc.encodeLettter(letter);
+    }
+  }
+  const posDF = DG.DataFrame.fromColumns(positions.map((v, i) => DG.Column.fromFloat32Array(df.columns.names()[i], v)));
+  return posDF;
 }
 
 /**
- * Unfolds a data frame into <category>-<value> format.
+ * Formats an adjacency matrix into <category1>-<category2>-<value> format.
  *
- * @param {DG.DataFrame} df A data frame to unfold.
+ * @param {DG.DataFrame} adjMatrix A data matrix to deal with.
  * @return {DG.DataFrame} The resulting data frame.
  */
-function melt(df: DG.DataFrame): DG.DataFrame {
-  let keys: string[] = [];
-  const values: Float32Array = new Float32Array(df.columns.length*df.rowCount);
-  let i = 0;
-
-  for (const c of df.columns.toList()) {
-    keys = keys.concat(Array<string>(c.length).fill(c.name));
-    values.set(c.getRawData(), i);
-    i += df.rowCount;
+function createNetwork(adjMatrix: DG.DataFrame): DG.DataFrame {
+  const nCols = adjMatrix.columns.length;
+  const nRows = adjMatrix.rowCount;
+
+  assert(nCols == nRows);
+
+  const pos1: Array<number> = [];
+  const pos2: Array<number> = [];
+  const weight: Array<number> = [];
+
+  for (let i = 0; i < nCols; ++i) {
+    const c = adjMatrix.columns.byIndex(i);
+
+    for (let j = i+1; j < nRows; ++j) {
+      const r = c.getRawData()[j];
+
+      if (Math.abs(r) > 0) {
+        pos1.push(i+1);
+        pos2.push(j+1);
+        weight.push(r);
+      }
+    }
   }
-  assert(keys.length == values.length);
-  return DG.DataFrame.fromColumns([DG.Column.fromStrings('keys', keys), DG.Column.fromFloat32Array('values', values)]);
+
+  const pos1Col = DG.Column.fromList('int', 'pos1', pos1);
+  const pos2Col = DG.Column.fromList('int', 'pos2', pos2);
+  const weightCol = DG.Column.fromList('double', 'weight', weight);
+
+  return DG.DataFrame.fromColumns([pos1Col, pos2Col, weightCol]);
 }
 
 /**
- * Calculates Spearman's rho rank correlation coefficient.
+ * Calculates Kendall's tau rank correlation matrix.
  *
  * @param {DG.DataFrame} df A data frame to process.
+ * @param {number} [alpha=0.05] The significance threshold.
+ * @param {number} [rAbsCutoff=0.5] The absolute R cutoff.
  * @return {DG.DataFrame} The correlation matrix.
  */
-function calcSpearmanRhoMatrix(df: DG.DataFrame): DG.DataFrame {
+function calcKendallTauMatrix(df: DG.DataFrame, alpha: number = 0.05, rAbsCutoff = 0.5): DG.DataFrame {
   const nItems = df.columns.length;
-  const rho = new Array(nItems).fill(0).map((_) => new Float32Array(nItems).fill(0));
+  const tau = new Array(nItems).fill(0).map((_) => new Float32Array(nItems).fill(0));
 
   for (let i = 0; i < nItems; ++i) {
     for (let j = i+1; j < nItems; ++j) {
-      rho[i][j] = df.columns.byIndex(i).stats.spearmanCorr(df.columns.byIndex(j));
-      rho[j][i] = rho[i][j];
+      const res = kendallsTau(df.columns.byIndex(i).getRawData(), df.columns.byIndex(j).getRawData());
+      tau[i][j] = (res.prob < alpha) && (Math.abs(res.test) >= rAbsCutoff) ? res.test : 0;
+      tau[j][i] = tau[i][j];
     }
   }
-  return matrix2DataFrame(rho);
+  return matrix2DataFrame(tau);
 }
 
 /**
- * Calculates Kendall's tau rank correlation coefficient.
+ * Calculates a correlation matrix via method chosen.
  *
- * @param {DG.DataFrame} df A data frame to process.
- * @param {number} [alpha=0.05] The significance threshold.
+ * @param {DG.DataFrame} df A data frame.
  * @return {DG.DataFrame} The correlation matrix.
  */
-function calcKendallTauMatrix(df: DG.DataFrame, alpha: number = 0.05): DG.DataFrame {
-  const nItems = df.columns.length;
-  const tau = new Array(nItems).fill(0).map((_) => new Float32Array(nItems).fill(0));
+function calcCorrelationMatrix(df: DG.DataFrame): DG.DataFrame {
+  return calcKendallTauMatrix(df);
+}
 
-  for (let i = 0; i < nItems; ++i) {
-    for (let j = i+1; j < nItems; ++j) {
-      const res = kendallsTau(df.columns.byIndex(i).getRawData(), df.columns.byIndex(j).getRawData());
-      tau[i][j] = res.prob < alpha ? res.test : 0;
-      tau[j][i] = tau[i][j];
+type Weights = {[pos: number]: number};
+type Guide = {[pos: number]: Weights};
+
+/**
+ * Calculates a dictionary with the keys containing the first correlating positions.
+ * Values correspond to a dictionary containing the positions and corresponding R-value
+ * which the given position correlating with.
+ *
+ * @param {DG.DataFrame} network A network to process.
+ * @return {Guide} The formatted dictionary.
+ */
+function calcGuide(network: DG.DataFrame): Guide {
+  assert(network.columns.length == 3);
+
+  const guide: Guide = {};
+  let [pos1Col, pos2Col, weightCol] = Array.from(network.columns);
+
+  pos1Col = pos1Col.getRawData();
+  pos2Col = pos2Col.getRawData();
+  weightCol = weightCol.getRawData();
+
+  function _addWeight(pos1: number, pos2: number, weight: number) {
+    if (guide[pos1] == undefined) {
+      guide[pos1] = {};
     }
+    guide[pos1][pos2] = weight;
   }
-  return matrix2DataFrame(tau);
+
+  for (let i = 0; i < network.rowCount; ++i) {
+    const [pos1, pos2, weight] = [pos1Col[i], pos2Col[i], weightCol[i]];
+    _addWeight(pos1, pos2, weight);
+    _addWeight(pos2, pos1, weight);
+  }
+  return guide;
+}
+
+function calcCorrelations(df: DG.DataFrame, positionColumns?: string[]): Guide {
+  const posDF = encodeSequences(df, positionColumns);
+  const ccDF = calcCorrelationMatrix(posDF);
+  const nwDF = createNetwork(ccDF);
+  const guide = calcGuide(nwDF);
+  return guide;
 }
 
 /**
- * Creates acorrelation plot and a box plot to perform correlation analysis.
+ * Formats correlating positions to place in the corresponding tooltips.
+ * Higlights correlating positions' headers.
  *
  * @export
- * @param {DG.Column} sequencesColumn A column containing amino acid sequences.
- * @return {[DG.Viewer, DG.Viewer]} These two plots.
+ * @class CorrelationAnalysisVisualizer
  */
-export function correlationAnalysisPlots(sequencesColumn: DG.Column): [DG.Viewer, DG.Viewer] {
-  const posDF = calcPositions(sequencesColumn);
-  const cpviewer = DG.Viewer.fromType(
-    DG.VIEWER.CORR_PLOT,
-    posDF,
-    {
-      'xColumnNames': posDF.columns.names(),
-      'yColumnNames': posDF.columns.names(),
-      'correlationType': 'Spearman',
-    });
-
-  const rhoDF = calcKendallTauMatrix(posDF);
-  const meltDF = melt(rhoDF);
-
-  const bpviewer = DG.Viewer.fromType(
-    DG.VIEWER.BOX_PLOT,
-    meltDF, {
-      'categoryColumnName': 'keys',
-      'valueColumnName': 'values',
-      'statistics': ['min', 'max', 'avg', 'med'],
-    });
-  return [cpviewer, bpviewer];
+export class CorrelationAnalysisVisualizer {
+  protected guide: Guide;
+  protected highlightedColumns: number[];
+
+  /**
+   * Creates an instance of CorrelationAnalysisVisualizer.
+   * @param {DG.DataFrame} df A data frame to take sequences from.
+   * @param {string[]} positionColumns Optional columns list to take the sequences from.
+   * @memberof CorrelationAnalysisVisualizer
+   */
+  constructor(df: DG.DataFrame, positionColumns: string[]) {
+    if (df) {
+      this.guide = calcCorrelations(df, positionColumns);
+      this.highlightedColumns = Object.keys(this.guide).map((v) => parseInt(v));
+    } else {
+      throw new Error('Dataframe was not found in the grid.');
+    }
+  }
+
+  /**
+   * Returns a dictionary with the correlating positions and their R-value.
+   *
+   * @readonly
+   * @type {Guide} The dictionary.
+   * @memberof CorrelationAnalysisVisualizer
+   */
+  get path(): Guide {
+    return this.guide;
+  }
+
+  /**
+   * Checks if the position column name is found among correlelating ones.
+   *
+   * @param {string} name The name of the column.
+   * @return {boolean} True if the position is correlating with any oter.
+   * @memberof CorrelationAnalysisVisualizer
+   */
+  public isPositionCorrelating(name: string): boolean {
+    return this.highlightedColumns.includes(parseInt(name));
+  }
 }

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

@@ -8,6 +8,15 @@ import {DimensionalityReducer} from '@datagrok-libraries/utils/src/reduce-dimens
 import {Measurer} from '@datagrok-libraries/utils/src/string-measure';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
+/**
+ * A worker to perform dimensionality reduction.
+ *
+ * @param {any[]} columnData The data to process.
+ * @param {string} method A method of dimensionality reduction.
+ * @param {string} measure A distance metrics.
+ * @param {number} cyclesCount Number of iterations to run.
+ * @return {Promise<unknown>} Resulting embedding.
+ */
 function createDimensinalityReducingWorker(
   columnData: any[],
   method: string,
@@ -38,7 +47,6 @@ function inferActivityColumnsName(table: DG.DataFrame): string | null {
   const re = /activity|ic50/i;
   for (const name of table.columns.names()) {
     if (name.match(re)) {
-      console.log(`${name} found.`);
       return name;
     }
   }
@@ -101,29 +109,27 @@ export async function createPeptideSimilaritySpaceViewer(
   // Add new axes.
   for (const axis of axesNames) {
     const col = table.col(axis);
+    const newCol = edf.getCol(axis);
 
-    if (col == null) {
-      table.columns.insert(edf.getCol(axis));
+    if (col != null) {
+      for (let i = 0; i < newCol.length; ++i) {
+        const v = newCol.get(i);
+        table.set(axis, i, v);
+      }
     } else {
-      table.columns.replace(col, edf.getCol(axis));
+      table.columns.insert(newCol);
     }
   }
 
-  // const viewer = DG.Viewer.scatterPlot(table, {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'});
   const viewerOptions = {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'};
-  const viewer = view !== null ?
-    view.addViewer(DG.VIEWER.SCATTER_PLOT, viewerOptions) : DG.Viewer.scatterPlot(table, viewerOptions);
-  // Fit view if needed.
-  /*if (zoom) {
-    viewer.zoom(
-      table.getCol('~X').min,
-      table.getCol('~Y').min,
-      table.getCol('~X').max,
-      table.getCol('~Y').max,
-    );
-  }*/
+  const viewer = DG.Viewer.scatterPlot(table, viewerOptions);
+
+  if (view !== null) {
+    view.addViewer(viewer);
+  }
+
   pi.close();
-  return (viewer as DG.ScatterPlotViewer);
+  return viewer;
 }
 
 /**

package/src/utils/split-aligned.ts

@@ -1,5 +1,13 @@
 import * as DG from 'datagrok-api/dg';
 
+/**
+ * Split aligned sequence string into separate parts containing amino acid residues.
+ *
+ * @export
+ * @param {DG.Column} peptideColumn Column containing aligned sequences.
+ * @param {boolean} [filter=true] Filter out columns with all the same residues.
+ * @return {[DG.DataFrame, number[]]} DataFrame containing split sequence and a list of invalid indexes.
+ */
 export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
   const splitPeptidesArray: string[][] = [];
   let currentSplitPeptide: string[];

package/src/viewers/logo-viewer.ts

@@ -7,6 +7,13 @@ import * as logojs from 'logojs-react';
 import {splitAlignedPeptides} from '../utils/split-aligned';
 import {ChemPalette} from '../utils/chem-palette';
 
+/**
+ * Logo viewer.
+ *
+ * @export
+ * @class Logo
+ * @extends {DG.JsViewer}
+ */
 export class Logo extends DG.JsViewer {
   initialized: boolean;
   option: any;
@@ -18,6 +25,11 @@ export class Logo extends DG.JsViewer {
   LET_COLORS: Array<any>;
   target: DG.DataFrame | undefined | null;
 
+  /**
+   * Creates an instance of Logo.
+   *
+   * @memberof Logo
+   */
   constructor() {
     super();
     this.initialized = false;
@@ -59,6 +71,11 @@ export class Logo extends DG.JsViewer {
     ];
   }
 
+  /**
+   * Initializer function.
+   *
+   * @memberof Logo
+   */
   init() {
     this.initialized = true;
     console.log('INIT');
@@ -69,6 +86,11 @@ export class Logo extends DG.JsViewer {
     this.root.style.maxHeight = '200px';
   }
 
+  /**
+   * Function to execute when the table is attached.
+   *
+   * @memberof Logo
+   */
   onTableAttached() {
     if (typeof this.dataFrame !== 'undefined') {
       if (!this.initialized) {
@@ -83,16 +105,32 @@ export class Logo extends DG.JsViewer {
     this.render();
   }
 
+  /**
+   * Function that is executed when the viewer is detached.
+   *
+   * @memberof Logo
+   */
   detach() {
     this.subs.forEach((sub) => sub.unsubscribe());
   }
 
+  /**
+   * Function that is executed when the viewer property is changed.
+   *
+   * @param {DG.Property} property
+   * @memberof Logo
+   */
   onPropertyChanged(property: DG.Property) {
     super.onPropertyChanged(property);
 
     this.render();
   }
 
+  /**
+   * Function that renders the viewer.
+   *
+   * @memberof Logo
+   */
   async render() {
     const bits = this.dataFrame!.selection;
     let selected = false;
@@ -113,11 +151,21 @@ export class Logo extends DG.JsViewer {
     }
   }
 
+  /**
+   * Create logo.
+   *
+   * @memberof Logo
+   */
   async findLogo() {
     this.getInfoFromDf();
     logojs.embedProteinLogo(this.root, {alphabet: this.LET_COLORS, ppm: this.ppm});
   }
 
+  /**
+   * Retrieves information for building logo from the dataframe.
+   *
+   * @memberof Logo
+   */
   getInfoFromDf() {
     let index: number = 0;
     this.ppm = [];

package/src/viewers/model.ts

@@ -3,6 +3,11 @@ import * as DG from 'datagrok-api/dg';
 import {describe} from '../describe';
 import {Subject} from 'rxjs';
 
+/**
+ * Model class for SAR viewers that retrieves and stores data.
+ *
+ * @class SARViewerModel
+ */
 class SARViewerModel {
   private viewerGrid: Subject<DG.Grid> = new Subject<DG.Grid>();
   private viewerVGrid: Subject<DG.Grid> = new Subject<DG.Grid>();
@@ -21,6 +26,11 @@ class SARViewerModel {
   private isUpdating = false;
   grouping: boolean;
 
+  /**
+   * Creates an instance of SARViewerModel.
+   *
+   * @memberof SARViewerModel
+   */
   constructor() {
     this.dataFrame = null;
     this.activityColumn = null;
@@ -35,6 +45,18 @@ class SARViewerModel {
     this.groupMapping$ = this.groupMapping.asObservable();
   }
 
+  /**
+   * Updates data with using specified parameters.
+   *
+   * @param {DG.DataFrame} df Working table.
+   * @param {string} activityCol Activity column name.
+   * @param {string} activityScaling Activity scaling method.
+   * @param {DG.Grid} sourceGrid Working table grid.
+   * @param {boolean} twoColorMode Bidirectional analysis enabled.
+   * @param {(DG.BitSet | null)} initialBitset Initial bitset.
+   * @param {boolean} grouping Grouping enabled.
+   * @memberof SARViewerModel
+   */
   async updateData(
     df: DG.DataFrame,
     activityCol: string,
@@ -54,6 +76,11 @@ class SARViewerModel {
     await this.updateDefault();
   }
 
+  /**
+   * Update data using current parameters.
+   *
+   * @memberof SARViewerModel
+   */
   async updateDefault() {
     if (
       this.dataFrame && this.activityColumn && this.activityScaling &&

package/src/viewers/sar-viewer.ts

@@ -6,6 +6,13 @@ import $ from 'cash-dom';
 
 import {model} from './model';
 
+/**
+ * Structure-activity relationship viewer.
+ *
+ * @export
+ * @class SARViewer
+ * @extends {DG.JsViewer}
+ */
 export class SARViewer extends DG.JsViewer {
   protected viewerGrid: DG.Grid | null;
   protected sourceGrid: DG.Grid | null;
@@ -25,6 +32,12 @@ export class SARViewer extends DG.JsViewer {
   // protected pValueThreshold: number;
   // protected amountOfBestAARs: number;
   // duplicatesHandingMethod: string;
+
+  /**
+   * Creates an instance of SARViewer.
+   *
+   * @memberof SARViewer
+   */
   constructor() {
     super();
 
@@ -51,6 +64,11 @@ export class SARViewer extends DG.JsViewer {
     this.sourceGrid = null;
   }
 
+  /**
+   * Initializes SARViewer.
+   *
+   * @memberof SARViewer
+   */
   init() {
     this._initialBitset = this.dataFrame!.filter.clone();
     this.initialized = true;
@@ -63,16 +81,32 @@ export class SARViewer extends DG.JsViewer {
     this.subs.push(model.groupMapping$.subscribe((data) => this.groupMapping = data));
   }
 
+  /**
+   * Function that is executed when the table is attached.
+   *
+   * @memberof SARViewer
+   */
   onTableAttached() {
     this.sourceGrid = this.view.grid;
     this.sourceGrid?.dataFrame?.setTag('dataType', 'peptides');
     this.render();
   }
 
+  /**
+   * Function that is executed when the viewer is detached from the table.
+   *
+   * @memberof SARViewer
+   */
   detach() {
     this.subs.forEach((sub) => sub.unsubscribe());
   }
 
+  /**
+   * Function that is executed when the property is changed.
+   *
+   * @param {DG.Property} property New property.
+   * @memberof SARViewer
+   */
   onPropertyChanged(property: DG.Property) {
     super.onPropertyChanged(property);
 
@@ -97,6 +131,12 @@ export class SARViewer extends DG.JsViewer {
     this.render();
   }
 
+  /**
+   * Filtering/selecting sequences with the specified amino acid residue at specified position.
+   *
+   * @private
+   * @memberof SARViewer
+   */
   private applyBitset() {
     if (
       this.dataFrame &&
@@ -133,6 +173,12 @@ export class SARViewer extends DG.JsViewer {
     }
   }
 
+  /**
+   * Selecting/filtering sequences according to the current bitset.
+   *
+   * @private
+   * @memberof SARViewer
+   */
   private sourceFilteringFunc() {
     if (this.filterMode) {
       this.dataFrame!.selection.setAll(false, false);
@@ -143,6 +189,13 @@ export class SARViewer extends DG.JsViewer {
     }
   }
 
+  /**
+   * Property panel accordion construction function.
+   *
+   * @private
+   * @param {DG.Accordion} accordion Accordion.
+   * @memberof SARViewer
+   */
   private accordionFunc(accordion: DG.Accordion) {
     if (accordion.context instanceof DG.RowGroup) {
       const originalDf: DG.DataFrame = DG.toJs(accordion.context.dataFrame);
@@ -203,7 +256,13 @@ export class SARViewer extends DG.JsViewer {
     }
   }
 
-  syncGridsFunc(sourceVertical: boolean) { //TODO: refactor
+  /**
+   * Function for viewer girds synchronization.
+   *
+   * @param {boolean} sourceVertical Event source is vertical viewer.
+   * @memberof SARViewer
+   */
+  syncGridsFunc(sourceVertical: boolean) { //TODO: refactor, move
     if (this.viewerGrid && this.viewerGrid.dataFrame && this.viewerVGrid && this.viewerVGrid.dataFrame) {
       if (sourceVertical) {
         const dfCell = this.viewerVGrid.dataFrame.currentCell;
@@ -245,8 +304,13 @@ export class SARViewer extends DG.JsViewer {
       }
     }
   }
-  // argument compute data can be used to just redraw grids.
-  // Probably iirelevant since mostly grids are updating themselves, and render is only used to update data.
+
+  /**
+   * Viewer render function.
+   *
+   * @param {boolean} [computeData=true] Recalculate data.
+   * @memberof SARViewer
+   */
   async render(computeData = true) {
     if (!this.initialized) {
       return;
@@ -282,8 +346,21 @@ export class SARViewer extends DG.JsViewer {
   }
 }
 
+/**
+ * Vertical structure activity relationship viewer.
+ *
+ * @export
+ * @class SARViewerVertical
+ * @extends {DG.JsViewer}
+ */
 export class SARViewerVertical extends DG.JsViewer {
   viewerVGrid: DG.Grid | null;
+
+  /**
+   * Creates an instance of SARViewerVertical.
+   *
+   * @memberof SARViewerVertical
+   */
   constructor() {
     super();
 
@@ -294,6 +371,11 @@ export class SARViewerVertical extends DG.JsViewer {
     }));
   }
 
+  /**
+   * Viewer render function.
+   *
+   * @memberof SARViewerVertical
+   */
   render() {
     if (this.viewerVGrid) {
       $(this.root).empty();