@datagrok/peptides 0.4.1 → 0.4.2

package/package.json

@@ -1,12 +1,12 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.4.1",
+	"version": "0.4.2",
 	"description": "",
 	"dependencies": {
 		"@keckelt/tsne": "^1.0.2",
 		"cash-dom": "latest",
 		"d3": "latest",
-		"datagrok-api": ">0.95.4",
+		"datagrok-api": ">=0.95.11",
 		"dayjs": "latest",
 		"jaro-winkler-typescript": "^1.0.1",
 		"jstat": "^1.9.5",

package/src/describe.ts

@@ -404,10 +404,10 @@ export async function describe(
     }
     if (
       !cell.isColHeader &&
-        cell.tableColumn !== null &&
-        cell.tableColumn.name == aminoAcidResidue &&
-        cell.cell.value !== null &&
-        cell.tableRowIndex !== null
+      cell.tableColumn !== null &&
+      cell.tableColumn.name == aminoAcidResidue &&
+      cell.cell.value !== null &&
+      cell.tableRowIndex !== null
     ) {
       if (grouping) {
         const currentGroup = groupDescription[cell.cell.value];

package/src/peptides.ts

@@ -1,4 +1,3 @@
-import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {createPeptideSimilaritySpaceViewer} from './utils/peptide-similarity-space';
@@ -6,13 +5,13 @@ import {addViewerToHeader} from './viewers/stacked-barchart-viewer';
 
 export class Peptides {
   async init(
-      tableGrid: DG.Grid,
-      view: DG.TableView,
-      currentDf: DG.DataFrame,
-      options: {[key: string]: string},
-      col: DG.Column,
-      activityColumnChoice: string
-    ) {
+    tableGrid: DG.Grid,
+    view: DG.TableView,
+    currentDf: DG.DataFrame,
+    options: {[key: string]: string},
+    col: DG.Column,
+    activityColumnChoice: string,
+  ) {
     for (let i = 0; i < tableGrid.columns.length; i++) {
       const col = tableGrid.columns.byIndex(i);
       if (col &&
@@ -30,7 +29,7 @@ export class Peptides {
     const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
 
     const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
-    const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
+    view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
 
     const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
       currentDf,
@@ -41,34 +40,37 @@ export class Peptides {
       view,
       `${activityColumnChoice}Scaled`,
     );
-    const psNode = view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
+    view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
 
     const StackedBarchartProm = currentDf.plot.fromType('StackedBarChartAA');
     addViewerToHeader(tableGrid, StackedBarchartProm);
 
     const hideIcon = ui.iconFA('window-close', () => { //undo?, times?
-        const viewers = [];
-        for (const viewer of view.viewers) {
-          if (viewer.type !== DG.VIEWER.GRID) {
-            viewers.push(viewer);
-          }
+      const viewers = [];
+      for (const viewer of view.viewers) {
+        if (viewer.type !== DG.VIEWER.GRID) {
+          viewers.push(viewer);
         }
-        viewers.forEach((v) => v.close());
+      }
+      viewers.forEach((v) => v.close());
 
-        const cols = (view.dataFrame.columns as DG.ColumnList);
-        for (const colName of cols.names()) {
-          if (!originalDfColumns.includes(colName)) {
-            cols.remove(colName);
-          }
+      const cols = (currentDf.columns as DG.ColumnList);
+      for (const colName of cols.names()) {
+        if (!originalDfColumns.includes(colName)) {
+          cols.remove(colName);
         }
+      }
 
-        tableGrid.setOptions({'colHeaderHeight': 20});
-        tableGrid.columns.setVisible(originalDfColumns);
+      currentDf.selection.setAll(false);
+      currentDf.filter.setAll(true);
 
-        view.setRibbonPanels(ribbonPanels);
+      tableGrid.setOptions({'colHeaderHeight': 20});
+      tableGrid.columns.setVisible(originalDfColumns);
+
+      view.setRibbonPanels(ribbonPanels);
     }, 'Close viewers and restore dataframe');
-    
+
     const ribbonPanels = view.getRibbonPanels();
     view.setRibbonPanels([[hideIcon]]);
   }
-}
+}

package/src/utils/chem-palette.ts

@@ -23,7 +23,12 @@ export class ChemPalette {
         if (s in ChemPalette.AAFullNames) {
           toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[s]])];
         }
-        const sketch = grok.chem.svgMol(ChemPalette.AASmiles[aar]);
+        const options = {
+          autoCrop: true,
+          autoCropMargin: 0,
+          suppressChiralText: true,
+        };
+        const sketch = grok.chem.svgMol(ChemPalette.AASmiles[aar], undefined, undefined, options);
         toDisplay.push(sketch);
       }
       ui.tooltip.show(ui.divV(toDisplay), x, y);

package/src/utils/correlation-analysis.ts

@@ -15,8 +15,8 @@ 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 {
-  return DG.DataFrame.fromColumns(matrix.map((v, i) => DG.Column.fromFloat32Array(`${i+1}`, v)));  
+export function matrix2DataFrame(matrix: Matrix): DG.DataFrame {
+  return DG.DataFrame.fromColumns(matrix.map((v, i) => DG.Column.fromFloat32Array(`${i+1}`, v)));
 }
 
 /**

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

@@ -10,15 +10,6 @@ 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';
 
-/**
- * Creates a worker to perform a dimensionality reduction.
- *
- * @param {any[]} columnData Samples to process.
- * @param {string} method Embedding method.
- * @param {string} measure Distance metric.
- * @param {number} cyclesCount Number of cycles to repeat.
- * @return {Promise<unknown>} Promise.
- */
 function createDimensinalityReducingWorker(
   columnData: any[],
   method: string,
@@ -65,6 +56,7 @@ function inferActivityColumnsName(table: DG.DataFrame): string | null {
  * @param {string} method Embedding method to apply.
  * @param {string} measure Distance metric.
  * @param {number} cyclesCount Number of cycles to repeat.
+ * @param {(DG.TableView | null)} view View to add scatter plot to
  * @param {(string | null)} [activityColumnName] Activity containing column to assign it to points radius.
  * @param {boolean} [zoom=false] Whether to fit view.
  * @return {Promise<DG.ScatterPlotViewer>} A viewer.
@@ -156,6 +148,7 @@ export class PeptideSimilaritySpaceWidget {
   /**
    * Creates an instance of PeptideSimilaritySpaceWidget.
    * @param {DG.Column} alignedSequencesColumn The column to get amino acid sequences from.
+   * @param {DG.TableView} view Current view
    * @memberof PeptideSimilaritySpaceWidget
    */
   constructor(alignedSequencesColumn: DG.Column, view: DG.TableView) {

package/src/widgets/analyze-peptides.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import { Peptides } from '../peptides';
+import {Peptides} from '../peptides';
 
 export async function analyzePeptidesWidget(
   col: DG.Column, view: DG.TableView, tableGrid: DG.Grid, currentDf: DG.DataFrame,
@@ -70,8 +70,8 @@ export async function analyzePeptidesWidget(
         'activityScalingMethod': activityScalingMethod.value,
       };
 
-      let peptides = new Peptides();
-      await peptides.init(tableGrid, view, currentDf, options, col, activityColumnChoice.value.name);      
+      const peptides = new Peptides();
+      await peptides.init(tableGrid, view, currentDf, options, col, activityColumnChoice.value.name);
 
       progress.close();
     } else {