@datagrok/peptides 0.2.0 → 0.3.0

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.2.0",
+	"version": "0.3.0",
 	"description": "",
 	"dependencies": {
 		"@keckelt/tsne": "^1.0.2",
@@ -13,7 +13,7 @@
 		"logojs-react": "^2.1.1",
 		"rxjs": "^6.5.5",
 		"umap-js": "^1.3.3",
-		"@datagrok-libraries/utils": ">=0.0.9",
+		"@datagrok-libraries/utils": ">=0.0.10",
 		"@datagrok-libraries/statistics": ">=0.1.4",
 		"@types/d3": "^7.0.0",
 		"@types/jquery": "^3.5.6"
@@ -52,4 +52,4 @@
 		"lint": "eslint \"./src/**/*.ts\"",
 		"lint-fix": "eslint \"./src/**/*.ts\" --fix"
 	}
-}
+}

package/src/package.ts

@@ -14,7 +14,8 @@ import {analyzePeptidesWidget} from './widgets/analyze-peptides';
 import {PeptideSimilaritySpaceWidget} from './utils/peptide-similarity-space';
 import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
-import { peptideMoleculeWidget } from './widgets/peptide-molecule';
+import {peptideMoleculeWidget} from './widgets/peptide-molecule';
+import {correlationAnalysisPlots} from './utils/correlation-analysis';
 
 export const _package = new DG.Package();
 let tableGrid: DG.Grid;
@@ -199,3 +200,15 @@ export async function peptideSpacePanel(col: DG.Column): Promise<DG.Widget> {
   const widget = new PeptideSimilaritySpaceWidget(col);
   return await widget.draw();
 }
+
+//name: Correllation analysis
+export async function correlationAnalysis() {
+  view = (grok.shell.v as DG.TableView);
+
+  const df = await grok.data.files.openTable('Demo:TestJobs:Files:DemoFiles/bio/peptides.csv');
+  const tview = grok.shell.addTableView(df);
+  const [cpviewer, bpviewer] = correlationAnalysisPlots(df.getCol('AlignedSequence'));
+
+  tview.dockManager.dock(cpviewer, 'right');
+  tview.dockManager.dock(bpviewer, 'down');
+}

package/src/utils/correlation-analysis.ts

@@ -0,0 +1,109 @@
+/* Do not change these import lines. Datagrok will import API library in exactly the same manner */
+//import * as grok from 'datagrok-api/grok';
+//import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {AlignedSequenceEncoder} from '@datagrok-libraries/utils/src/sequence-encoder';
+import {assert, transposeMatrix, matrix2DataFrame} from '@datagrok-libraries/utils/src/operations';
+import {Vector} from '@datagrok-libraries/utils/src/type_declarations';
+
+/**
+ * Encodes amino acid sequences into a numeric representation.
+ *
+ * @export
+ * @param {DG.Column} col A column containing the sequences.
+ * @return {DG.DataFrame} The resulting data frame.
+ */
+export 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);
+}
+
+/**
+ * Unfolds a data frame into <category>-<value> format.
+ *
+ * @export
+ * @param {DG.DataFrame} df A data frame to unfold.
+ * @return {DG.DataFrame} The resulting data frame.
+ */
+export 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;
+  }
+  assert(keys.length == values.length);
+  return DG.DataFrame.fromColumns([DG.Column.fromStrings('keys', keys), DG.Column.fromFloat32Array('values', values)]);
+}
+
+/*export async function calcSpearmanRhoMatrixExt(positions: Matrix): Promise<Matrix> {
+  const Spearman = require('spearman-rho');
+  const nItems = positions.length;
+  const rho = 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] = await(new Spearman(positions[i], positions[j])).calc();
+      rho[j][i] = rho[i][j];
+    }
+  }
+  return rho;
+}*/
+
+/**
+ * Calculates Spearman's rho rank correlation coefficient.
+ *
+ * @export
+ * @param {DG.DataFrame} df A data frame to process.
+ * @return {DG.DataFrame} The correlation matrix.
+ */
+export function calcSpearmanRhoMatrix(df: DG.DataFrame): DG.DataFrame {
+  const nItems = df.columns.length;
+  const rho = 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];
+    }
+  }
+  return matrix2DataFrame(rho);
+}
+
+/**
+ * Creates acorrelation plot and a box plot to perform correlation analysis.
+ *
+ * @export
+ * @param {DG.Column} sequencesColumn A column containing amino acid sequences.
+ * @return {[DG.Viewer, DG.Viewer]} These two plots.
+ */
+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 = calcSpearmanRhoMatrix(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];
+}