@datagrok/peptides 1.14.0 → 1.15.0

package/dist/package.js.LICENSE.txt

@@ -0,0 +1,51 @@
+/**
+ * @license
+ *
+ * Copyright 2019 Google LLC. All Rights Reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ==============================================================================
+ */
+
+/**
+ * @license
+ * BSD 3-Clause License
+ *
+ * Copyright (c) 2017, Leland McInnes
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * * Redistributions of source code must retain the above copyright notice, this
+ *   list of conditions and the following disclaimer.
+ *
+ * * Redistributions in binary form must reproduce the above copyright notice,
+ *   this list of conditions and the following disclaimer in the documentation
+ *   and/or other materials provided with the distribution.
+ *
+ * * Neither the name of the copyright holder nor the names of its
+ *   contributors may be used to endorse or promote products derived from
+ *   this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */

package/files/help/logo-summary-table.md

@@ -0,0 +1,23 @@
+# Logo Summary Table
+
+Logo Summary Table shows WebLogo, activity distribution and statistics for each of the clusters in data. Statistics include 
+mean difference, p-value, count and ratio.
+
+# Responsiveness
+
+Logo Summary Table reacts to filters applied to the data and shows only clusters of filtered rows. In this case WebLogo,
+activity distribution and statistics are calculated with respect to filtered rows.
+
+## Interactivity
+
+Logo Summary Tabl viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                               |
+|------------------|-------------------------------|
+| Click            | Single selection of Cluster   |
+| Ctrl+Click       | Toggle Cluster selection state|
+| Shift+Click      | Add Cluster to selection      |
+| Ctrl+Shift+Click | Deselect Cluster              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding 
+points on other viewers.

package/files/help/monomer-position.md

@@ -0,0 +1,31 @@
+# Monomer-Position viewer
+
+Monomer-Position viewer is a matrix-like grid, where rows correspond to monomers and columns to positions. This viewer works in two modes: Mutation Cliffs and Invariant Map.
+
+## Mutation Cliffs mode
+
+Mutation Cliffs mode highlights the most signficant monomer-position pairs. The significance of the monomer-position is 
+color-coded with blue for negative mean difference of the sequences containing monomer-position vs. rest of the sequences,
+and red for positive mean difference. Color intensity is defined by p-value. The size of the circle represents the value of mean difference:
+smaller circles represent low mean difference values; large circles represent hight mean difference values. Some of the 
+cells contain number of unique sequences for given monomer-position, that form Mutation Cliff pairs.
+
+## Invariant Map mode
+
+Invariant Map mode shows number of sequences that contain monomer-position. Cells are color-coded based on the aggregation 
+function on some numeric column. By default average scaled activity values for given monomer-position is used. Column and
+aggregation function can be changed in viewer properties.
+
+## Interactivity
+
+Monomer-Position viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                                        |
+|------------------|----------------------------------------|
+| Click            | Single selection of Monomer-Position   |
+| Ctrl+Click       | Toggle Monomer-Position selection state|
+| Shift+Click      | Add Monomer-Position to selection      |
+| Ctrl+Shift+Click | Deselect Monomer-Position              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding
+points on other viewers.

package/files/help/most-potent-residues.md

@@ -0,0 +1,17 @@
+# Most Potent Residues
+
+Most Potent Residues viewer for each position finds the most potent monomer and shows statistics for the monomer-position. Statistics include mean difference, p-value, count and ratio.
+
+## Interactivity
+
+Most Potent Residues viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                                        |
+|------------------|----------------------------------------|
+| Click            | Single selection of Monomer-Position   |
+| Ctrl+Click       | Toggle Monomer-Position selection state|
+| Shift+Click      | Add Monomer-Position to selection      |
+| Ctrl+Shift+Click | Deselect Monomer-Position              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding 
+points on other viewers.

package/files/icons/ribbon/logo-summary-viewer.svg

@@ -0,0 +1,8 @@
+<svg width="36" height="36" viewBox="0 0 36 36" fill="none" xmlns="http://www.w3.org/2000/svg">
+<path d="M20.6603 18.7754C20.9386 18.7754 21.1871 18.697 21.4058 18.5401C21.6244 18.3832 21.7984 18.1622 21.9276 17.877C22.0618 17.5918 22.1338 17.2602 22.1438 16.8824H24C23.9901 17.6667 23.836 18.369 23.5378 18.9893C23.2396 19.6096 22.842 20.1016 22.345 20.4652C21.853 20.8217 21.3014 21 20.6901 21C20.0689 21 19.5272 20.8503 19.065 20.5508C18.6028 20.2513 18.2176 19.8342 17.9095 19.2995C17.6063 18.7647 17.3777 18.1444 17.2236 17.4385C17.0745 16.7326 17 15.9768 17 15.1711V14.8289C17 14.0232 17.0745 13.2674 17.2236 12.5615C17.3777 11.8556 17.6063 11.2353 17.9095 10.7005C18.2176 10.1658 18.6028 9.74866 19.065 9.4492C19.5272 9.14973 20.0664 9 20.6826 9C21.3337 9 21.9052 9.18182 22.3972 9.54545C22.8942 9.90909 23.2819 10.4225 23.5602 11.0856C23.8435 11.7487 23.9901 12.5294 24 13.4278H22.1438C22.1338 13.0143 22.0692 12.6435 21.9499 12.3155C21.8307 11.9875 21.6617 11.7237 21.443 11.5241C21.2244 11.3244 20.9585 11.2246 20.6454 11.2246C20.3124 11.2246 20.0341 11.3244 19.8104 11.5241C19.5918 11.7237 19.4203 11.9982 19.2961 12.3476C19.1768 12.6898 19.0923 13.0749 19.0426 13.5027C18.9979 13.9234 18.9755 14.3654 18.9755 14.8289V15.1711C18.9755 15.6417 18.9979 16.0909 19.0426 16.5187C19.0923 16.9465 19.1768 17.3316 19.2961 17.6738C19.4203 18.0089 19.5918 18.2763 19.8104 18.4759C20.0341 18.6756 20.3174 18.7754 20.6603 18.7754Z" fill="#40607F"/>
+<path d="M9.87361 5.73214L5.24535 21H2L8.06691 3H10.1413L9.87361 5.73214ZM13.7435 21L9.09294 5.73214L8.81413 3H10.8996L17 21H13.7435ZM13.5316 14.3118V16.9945H4.82156V14.3118H13.5316Z" fill="#40607F"/>
+<path d="M34 7V21H31.8769L27.1154 11.2885V21H25V7H27.1154L31.8923 16.7212V7H34Z" fill="#40607F" fill-opacity="0.5"/>
+<path d="M6.44251 31.0838L8.63182 23H9.81707L9.89257 24.7033L7.55226 33H6.29907L6.44251 31.0838ZM5.06098 23L6.85772 31.0563V33H5.49129L3 23H5.06098ZM12.1649 31.022L13.9315 23H16L13.5087 33H12.1423L12.1649 31.022ZM10.3833 23L12.5726 31.1113L12.7009 33H11.4477L9.11498 24.6964L9.20557 23H10.3833Z" fill="#40607F" fill-opacity="0.5"/>
+<path d="M21.3392 31.554V24H23V32.8843H21.5016L21.3392 31.554ZM17 29.8303V29.7089C17 29.2307 17.0583 28.7969 17.1748 28.4075C17.2955 28.0141 17.4703 27.6767 17.6993 27.3952C17.9282 27.1138 18.205 26.8959 18.5297 26.7416C18.8585 26.5874 19.231 26.5103 19.6472 26.5103C20.051 26.5103 20.4027 26.5855 20.7024 26.7359C21.0062 26.8862 21.2643 27.1003 21.4766 27.3779C21.693 27.6555 21.8658 27.9852 21.9948 28.367C22.1238 28.7449 22.2175 29.1613 22.2758 29.6163V29.946C22.2175 30.3895 22.1238 30.7963 21.9948 31.1665C21.8658 31.5366 21.693 31.8605 21.4766 32.1382C21.2643 32.412 21.0062 32.624 20.7024 32.7744C20.3985 32.9248 20.0427 33 19.6348 33C19.2227 33 18.8522 32.921 18.5234 32.7629C18.1988 32.6048 17.922 32.383 17.693 32.0977C17.4683 31.8123 17.2955 31.4769 17.1748 31.0913C17.0583 30.7057 17 30.2853 17 29.8303ZM18.6545 29.7089V29.8303C18.6545 30.1003 18.6795 30.3528 18.7294 30.588C18.7794 30.8233 18.8606 31.0315 18.9729 31.2127C19.0853 31.3901 19.2289 31.5289 19.4037 31.6292C19.5827 31.7294 19.7992 31.7796 20.0531 31.7796C20.3777 31.7796 20.6441 31.714 20.8522 31.5829C21.0645 31.4479 21.2289 31.2648 21.3455 31.0334C21.462 30.7982 21.5369 30.5341 21.5702 30.241V29.3329C21.5536 29.1015 21.5099 28.8875 21.4391 28.6909C21.3725 28.4942 21.2768 28.3246 21.1519 28.1819C21.0312 28.0392 20.8814 27.9274 20.7024 27.8464C20.5234 27.7654 20.3111 27.7249 20.0656 27.7249C19.8117 27.7249 19.5952 27.777 19.4162 27.8811C19.2373 27.9814 19.0916 28.1221 18.9792 28.3033C18.8668 28.4846 18.7836 28.6947 18.7294 28.9338C18.6795 29.1729 18.6545 29.4312 18.6545 29.7089Z" fill="#40607F" fill-opacity="0.7"/>
+<path d="M28.9545 33H26.1L26.1182 31.3681H28.9545C29.7242 31.3681 30.3697 31.2271 30.8909 30.9451C31.4121 30.658 31.8061 30.2475 32.0727 29.7136C32.3394 29.1747 32.4727 28.53 32.4727 27.7795V27.2129C32.4727 26.6337 32.397 26.1225 32.2455 25.6793C32.0939 25.236 31.8697 24.8633 31.5727 24.5611C31.2818 24.2589 30.9212 24.0298 30.4909 23.8736C30.0606 23.7175 29.5667 23.6394 29.0091 23.6394H26.0455V22H29.0091C29.8939 22 30.7 22.1234 31.4273 22.3702C32.1606 22.617 32.7939 22.9721 33.3273 23.4354C33.8667 23.8938 34.2788 24.4428 34.5636 25.0824C34.8545 25.7221 35 26.4373 35 27.228V27.7795C35 28.5652 34.8545 29.2804 34.5636 29.9251C34.2788 30.5648 33.8667 31.1138 33.3273 31.5721C32.7939 32.0304 32.1576 32.383 31.4182 32.6298C30.6788 32.8766 29.8576 33 28.9545 33ZM27.5 22V33H25V22H27.5Z" fill="#40607F"/>
+</svg>

package/files/icons/ribbon/peptide-sar-vertical-viewer.svg

@@ -0,0 +1,10 @@
+<svg width="36" height="36" viewBox="0 0 36 36" fill="none" xmlns="http://www.w3.org/2000/svg">
+<path d="M30 7.5C30 6.94772 29.5523 6.5 29 6.5H15C14.4477 6.5 14 6.94772 14 7.5V7.5C14 8.05228 14.4477 8.5 15 8.5H29C29.5523 8.5 30 8.05228 30 7.5V7.5Z" fill="#B3BFCC"/>
+<path d="M30 14.5C30 13.9477 29.5523 13.5 29 13.5H15C14.4477 13.5 14 13.9477 14 14.5V14.5C14 15.0523 14.4477 15.5 15 15.5H29C29.5523 15.5 30 15.0523 30 14.5V14.5Z" fill="#B3BFCC"/>
+<path d="M30 21.5C30 20.9477 29.5523 20.5 29 20.5H15C14.4477 20.5 14 20.9477 14 21.5V21.5C14 22.0523 14.4477 22.5 15 22.5H29C29.5523 22.5 30 22.0523 30 21.5V21.5Z" fill="#B3BFCC"/>
+<path d="M30 28.5C30 27.9477 29.5523 27.5 29 27.5H15C14.4477 27.5 14 27.9477 14 28.5V28.5C14 29.0523 14.4477 29.5 15 29.5H29C29.5523 29.5 30 29.0523 30 28.5V28.5Z" fill="#B3BFCC"/>
+<circle cx="8" cy="7.5" r="3" fill="#40607F"/>
+<circle cx="8" cy="14.5" r="1.5" fill="#7990A5"/>
+<circle cx="8" cy="28.5" r="2" fill="#7990A5"/>
+<circle cx="8" cy="21.5" r="2" fill="#40607F"/>
+</svg>

package/files/icons/ribbon/peptide-sar-viewer.svg

@@ -0,0 +1,11 @@
+<svg width="36" height="36" viewBox="0 0 36 36" fill="none" xmlns="http://www.w3.org/2000/svg">
+<circle cx="9" cy="9.5" r="3" fill="#40607F"/>
+<circle cx="18" cy="9.5" r="2" fill="#7990A5"/>
+<circle cx="9" cy="18" r="2" fill="#7990A5"/>
+<circle cx="9" cy="27" r="2" fill="#7990A5"/>
+<circle cx="18" cy="18" r="1.5" fill="#7990A5"/>
+<circle cx="28" cy="18" r="2" fill="#7990A5"/>
+<circle cx="28" cy="27" r="1.5" fill="#7990A5"/>
+<circle cx="28" cy="9.5" r="3" fill="#40607F"/>
+<circle cx="18" cy="27" r="3" fill="#40607F"/>
+</svg>

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.14.0",
+  "version": "1.15.0",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"
@@ -13,10 +13,10 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.38.2",
-    "@datagrok-libraries/ml": "^6.3.40",
+    "@datagrok-libraries/bio": "^5.38.11",
+    "@datagrok-libraries/ml": "^6.3.48",
     "@datagrok-libraries/statistics": "^1.2.7",
-    "@datagrok-libraries/utils": "^4.1.13",
+    "@datagrok-libraries/utils": "^4.1.15",
     "@datagrok-libraries/tutorials": "^1.3.7",
     "cash-dom": "^8.1.5",
     "datagrok-api": "^1.16.4",

package/src/model.ts

@@ -33,6 +33,10 @@ import {findMutations} from './utils/algorithms';
 import {createDistanceMatrixWorker} from './utils/worker-creator';
 import {getSelectionWidget} from './widgets/selection';
 
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
+import {DimReductionMethods, ITSNEOptions, IUMAPOptions} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+
 export type SummaryStats = {
   minCount: number, maxCount: number,
   minMeanDifference: number, maxMeanDifference: number,
@@ -88,6 +92,7 @@ export class PeptidesModel {
   subs: rxjs.Subscription[] = [];
   isHighlighting: boolean = false;
   latestSelectionItem: (type.SelectionItem & {kind: SELECTION_MODE | 'Cluster'}) | null = null;
+  controlFire: boolean = false;
 
   private constructor(dataFrame: DG.DataFrame) {
     this.df = dataFrame;
@@ -418,7 +423,7 @@ export class PeptidesModel {
   }
 
   createAccordion(): DG.Accordion | null {
-    const trueModel: PeptidesModel | undefined = grok.shell.t.temp[PeptidesModel.modelName];
+    const trueModel: PeptidesModel | undefined = grok.shell.t?.temp[PeptidesModel.modelName];
     if (!trueModel)
       return null;
 
@@ -519,6 +524,7 @@ export class PeptidesModel {
       const newColCat = newCol.categories;
       const newColData = newCol.getRawData();
       col = cols.addNew(newCol.name, newCol.type).init((i) => newColCat[newColData[i]]);
+      col.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
       CR.setMonomerRenderer(col, this.alphabet);
     }
     this.df.name = name;
@@ -970,14 +976,22 @@ export class PeptidesModel {
         pane.expanded = true;
     };
 
-    DG.debounce(selection.onChanged, 500).subscribe(() => {
+    selection.onChanged.subscribe(() => {
+      if (this.controlFire) {
+        this.controlFire = false;
+        return;
+      }
       if (!this.isUserChangedSelection)
         selection.copyFrom(getLatestSelection(), false);
       showAccordion();
       this.isUserChangedSelection = true;
     });
 
-    DG.debounce(filter.onChanged, 500).subscribe(() => {
+    filter.onChanged.subscribe(() => {
+      if (this.controlFire) {
+        this.controlFire = false;
+        return;
+      }
       const lstViewer = this.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable | null;
       if (lstViewer !== null && typeof lstViewer.model !== 'undefined') {
         lstViewer.createLogoSummaryTableGrid();
@@ -994,6 +1008,13 @@ export class PeptidesModel {
     this.df.selection.fireChanged();
     if (fireFilterChanged)
       this.df.filter.fireChanged();
+
+    // Fire bitset changed event again to update UI
+    this.controlFire = true;
+    this.df.selection.fireChanged();
+    if (fireFilterChanged)
+      this.df.filter.fireChanged();
+
     this.headerSelectedMonomers = calculateSelected(this.df);
   }
 
@@ -1162,6 +1183,7 @@ export class PeptidesModel {
   addNewCluster(clusterName: string): void {
     const newClusterCol = DG.Column.fromBitSet(clusterName, this.getCompoundBitset());
     newClusterCol.setTag(C.TAGS.CUSTOM_CLUSTER, '1');
+    newClusterCol.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
     this.df.columns.add(newClusterCol);
     this.analysisView.grid.col(newClusterCol.name)!.visible = false;
   }
@@ -1230,4 +1252,17 @@ export class PeptidesModel {
     }
     return selection;
   }
+
+  async addSequenceSpace(): Promise<void> {
+    const seqSpaceParams: {table: DG.DataFrame, molecules: DG.Column, methodName: DimReductionMethods,
+      similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames, plotEmbeddings: boolean,
+      sparseMatrixThreshold?: number, options?: IUMAPOptions | ITSNEOptions} =
+      {table: this.df, molecules: this.df.getCol(this.settings.sequenceColumnName!), methodName: DimReductionMethods.UMAP,
+        similarityMetric: MmDistanceFunctionsNames.MONOMER_CHEMICAL_DISTANCE, plotEmbeddings: true, sparseMatrixThreshold: 0.8,
+        options: {}};
+    const seqSpaceViewer: DG.ScatterPlotViewer | undefined = await grok.functions.call('Bio:sequenceSpaceTopMenu', seqSpaceParams);
+    if (typeof seqSpaceViewer === 'undefined')
+      return;
+    this.analysisView.dockManager.dock(seqSpaceViewer, DG.DOCK_TYPE.RIGHT, this.findViewerNode(VIEWER_TYPE.LOGO_SUMMARY_TABLE), 'Sequence space');
+  }
 }

package/src/package-test.ts

@@ -1,14 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 
-// import './tests/core';
+import './tests/core';
 //FIXME: fails on CI; crashes browser
 // import './tests/peptide-space-test';
 import './tests/algorithms';
-// import './tests/viewers';
-// import './tests/widgets';
-// import './tests/table-view';
-// import './tests/model';
+import './tests/viewers';
+import './tests/widgets';
+import './tests/table-view';
+import './tests/model';
 
 export const _package = new DG.Package();
 export {tests};

package/src/tests/core.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expect, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, awaitCheck, delay, after} from '@datagrok-libraries/utils/src/test';
 
 import {_package} from '../package-test';
 import {startAnalysis} from '../widgets/peptides';
@@ -38,15 +38,9 @@ category('Core', () => {
     model = await startAnalysis(
       simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, C.SCALING_METHODS.MINUS_LG);
     expect(model instanceof PeptidesModel, true, 'Model is null');
-    let overlayInit = false;
-    grok.log.debug('Waiting for overlay...');
-    model!._analysisView!.grid.onAfterDrawOverlay.subscribe(() => {
-      overlayInit = true;
-      grok.log.debug('Overlay initialized');
-    });
-
+ 
     model!.mutationCliffsSelection = {'11': ['D']};
-    await delay(500);
+    await delay(3000)
   });
 
   test('Start analysis: сomplex', async () => {
@@ -64,16 +58,9 @@ category('Core', () => {
     model = await startAnalysis(
       complexActivityCol, complexAlignedSeqCol, null, complexTable, complexScaledCol, C.SCALING_METHODS.MINUS_LG);
     expect(model instanceof PeptidesModel, true, 'Model is null');
-    let overlayInit = false;
-    model!._analysisView!.grid.onAfterDrawOverlay.subscribe(() => {
-      overlayInit = true;
-      grok.log.debug('Overlay initialized');
-    });
-
-    if (model !== null)
-      model.mutationCliffsSelection = {'13': ['-']};
 
-    await delay(500);
+    model!.mutationCliffsSelection = {'13': ['-']};
+    await delay(3000)
   });
 
   test('Save and load project', async () => {
@@ -105,7 +92,7 @@ category('Core', () => {
     const sp = await grok.dapi.projects.save(project);
 
     v.close();
-    await awaitCheck(() => typeof grok.shell.tableView('Peptides analysis') === 'undefined', 'Table never closed', 2000);
+    await awaitCheck(() => typeof grok.shell.tableView('Peptides analysis') === 'undefined', 'Table never closed', 3000);
 
     await sp.open();
     v = grok.shell.getTableView('Peptides analysis');
@@ -113,8 +100,6 @@ category('Core', () => {
     await grok.dapi.layouts.delete(sl);
     await grok.dapi.tables.delete(sti);
     await grok.dapi.projects.delete(sp);
-
-    await delay(500);
   });
 
   test('Cluster stats - Benchmark HELM 5k', async () => {

package/src/tests/model.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, before, expect, expectFloat, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {category, test, before, expect, expectFloat, awaitCheck, delay, after} from '@datagrok-libraries/utils/src/test';
 import {_package} from '../package-test';
 import {PeptidesModel, VIEWER_TYPE, getAggregatedColName} from '../model';
 import {startAnalysis} from '../widgets/peptides';
@@ -38,6 +38,8 @@ category('Model: Settings', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('Activity scaling', async () => {
     const getError = (row: number, method: SCALING_METHODS): string =>
       `Activity mismatch at row ${row} for scaling method '${method}'`;

package/src/tests/table-view.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, before, expect, delay} from '@datagrok-libraries/utils/src/test';
+import {category, test, before, expect, delay, after} from '@datagrok-libraries/utils/src/test';
 import {_package} from '../package-test';
 import {CLUSTER_TYPE, PeptidesModel} from '../model';
 import {startAnalysis} from '../widgets/peptides';
@@ -39,6 +39,8 @@ category('Table view', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('Tooltip', async () => {
     expect(model.showMonomerTooltip(firstPair.monomerOrCluster, 0, 0), true,
       `Couldn't structure for monomer ${firstPair.monomerOrCluster}`);
@@ -65,7 +67,6 @@ category('Table view', () => {
 
     // Select first monomer-position pair
     model.modifyMutationCliffsSelection(firstPair);
-    await delay(500);
     expect(model.mutationCliffsSelection[firstPair.positionOrClusterType].includes(firstPair.monomerOrCluster), true,
       `Monomer ${firstPair.monomerOrCluster} is not selected at position ${firstPair.positionOrClusterType}`);
     expect(selection.trueCount, firstPair.mcCount, `Selection count is not equal to ${firstPair.mcCount} ` +
@@ -73,7 +74,6 @@ category('Table view', () => {
 
     // Select second monomer-position pair
     model.modifyMutationCliffsSelection(secondPair, {shiftPressed: true, ctrlPressed: false});
-    await delay(500);
     expect(model.mutationCliffsSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), true,
       `Monomer ${secondPair.monomerOrCluster} is not selected at position ${secondPair.positionOrClusterType}`);
     expect(selection.trueCount, secondPair.mcCount + firstPair.mcCount, `Selection count is not equal ` +
@@ -82,7 +82,6 @@ category('Table view', () => {
 
     // Deselect second monomer-position pair
     model.modifyMutationCliffsSelection(secondPair, {shiftPressed: true, ctrlPressed: true});
-    await delay(500);
     expect(model.mutationCliffsSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), false,
       `Monomer ${secondPair.monomerOrCluster} is still selected at position ${secondPair.positionOrClusterType} after deselection`);
     expect(selection.trueCount, firstPair.mcCount, `Selection count is not equal to ${firstPair.mcCount} ` +
@@ -90,7 +89,6 @@ category('Table view', () => {
 
     // Clear monomer-position selection
     model.initMutationCliffsSelection();
-    await delay(500);
     for (const [position, selectedMonomers] of Object.entries(model.mutationCliffsSelection)) {
       expect(selectedMonomers.length, 0, `Selection is not empty for position ${position} after clearing ` +
         `monomer-position selection`);
@@ -99,7 +97,6 @@ category('Table view', () => {
 
     // Select first cluster
     model.modifyClusterSelection(firstCluster);
-    await delay(500);
     expect(model.clusterSelection[firstCluster.positionOrClusterType].includes(firstCluster.monomerOrCluster), true,
       `Cluster ${firstCluster.monomerOrCluster} is not selected`);
     expect(selection.trueCount, firstCluster.count, `Selection count is not equal to ${firstCluster.count} for ` +
@@ -107,7 +104,6 @@ category('Table view', () => {
 
     // Select second cluster
     model.modifyClusterSelection(secondCluster, {shiftPressed: true, ctrlPressed: false});
-    await delay(500);
     expect(model.clusterSelection[secondCluster.positionOrClusterType].includes(secondCluster.monomerOrCluster), true,
       `Cluster ${secondCluster.monomerOrCluster} is not selected`);
     expect(selection.trueCount, firstCluster.count + secondCluster.count, `Selection count is not equal to ` +
@@ -115,7 +111,6 @@ category('Table view', () => {
 
     // Deselect first cluster
     model.modifyClusterSelection(firstCluster, {shiftPressed: true, ctrlPressed: true});
-    await delay(500);
     expect(model.clusterSelection[firstCluster.positionOrClusterType].includes(firstCluster.monomerOrCluster), false,
       `Cluster ${firstCluster.monomerOrCluster} is still selected after deselection`);
     expect(selection.trueCount, secondCluster.count, `Selection count is not equal to ${secondCluster.count} for ` +
@@ -123,7 +118,6 @@ category('Table view', () => {
 
     // Clear selection
     model.initClusterSelection();
-    await delay(500);
     expect(model.isClusterSelectionEmpty, true, `Selection is not empty after clearing cluster selection`);
     expect(selection.trueCount, 0, `Selection count is not equal to 0 after clearing cluster selection`);
   });
@@ -136,7 +130,6 @@ category('Table view', () => {
 
     // Select by second monomer-position pair
     model.modifyInvariantMapSelection(secondPair);
-    await delay(500);
     expect(model.invariantMapSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), true,
       `Monomer ${secondPair.monomerOrCluster} is not filtered at position ${secondPair.positionOrClusterType}`);
     expect(selection.trueCount, secondPair.imCount, `Filter count is not equal to ${secondPair.imCount} ` +
@@ -144,7 +137,6 @@ category('Table view', () => {
 
     // Select by first monomer-position pair
     model.modifyInvariantMapSelection(firstPair, {shiftPressed: true, ctrlPressed: false});
-    await delay(500);
     expect(model.invariantMapSelection[firstPair.positionOrClusterType].includes(firstPair.monomerOrCluster), true,
       `Monomer ${firstPair.monomerOrCluster} is not filtered at position ${firstPair.positionOrClusterType}`);
     expect(selection.trueCount, secondPair.imCount, `Filter count is not equal to ${secondPair.imCount} ` +
@@ -152,7 +144,6 @@ category('Table view', () => {
 
     // Deselect filter for second monomer-position pair
     model.modifyInvariantMapSelection(secondPair, {shiftPressed: true, ctrlPressed: true});
-    await delay(500);
     expect(model.invariantMapSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), false,
       `Monomer ${secondPair.monomerOrCluster} is still filtered at position ${secondPair.positionOrClusterType} after ` +
       `deselection`);
@@ -162,7 +153,6 @@ category('Table view', () => {
 
     // Clear selection
     model.initInvariantMapSelection();
-    await delay(500);
     expect(selection.trueCount, 0, `Filter count is not equal to ${0} after clearing monomer-position filter`);
 
     for (const [position, filteredMonomers] of Object.entries(model.invariantMapSelection)) {

package/src/tests/viewers.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, delay, expect, test, testViewer} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, testViewer} from '@datagrok-libraries/utils/src/test';
 import {aligned1} from './test-data';
 import {CLUSTER_TYPE, PeptidesModel, VIEWER_TYPE} from '../model';
 import {_package} from '../package-test';
@@ -50,6 +50,8 @@ category('Viewers: Monomer-Position', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('Tooltip', async () => {
     const cellCoordinates = {col: '9', row: 6};
     const gc = mpViewer.viewerGrid.cell(cellCoordinates.col, cellCoordinates.row);
@@ -102,6 +104,8 @@ category('Viewers: Most Potent Residues', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('Tooltip', async () => {
     const cellCoordinates = {col: 'Diff', row: 6};
     const gc = mprViewer.viewerGrid.cell(cellCoordinates.col, cellCoordinates.row);
@@ -139,6 +143,8 @@ category('Viewers: Logo Summary Table', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('Properties', async () => {
     // Change Logo Summary Table Web Logo Mode property to full
     const webLogoMode = lstViewer.getProperty(LST_PROPERTIES.WEB_LOGO_MODE);

package/src/tests/widgets.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, before, expect, delay} from '@datagrok-libraries/utils/src/test';
+import {category, test, before, expect, delay, after} from '@datagrok-libraries/utils/src/test';
 import {_package} from '../package-test';
 import {CLUSTER_TYPE, PeptidesModel, VIEWER_TYPE} from '../model';
 import {scaleActivity} from '../utils/misc';
@@ -40,6 +40,8 @@ category('Widgets: Settings', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('UI', async () => {
     const settingsElements = getSettingsDialog(model);
 
@@ -83,6 +85,8 @@ category('Widgets: Distribution panel', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('UI', async () => {
     getDistributionWidget(model.df, model);
   });
@@ -113,6 +117,8 @@ category('Widgets: Mutation cliffs', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('UI', async () => {
     mutationCliffsWidget(model.df, model);
   });
@@ -143,6 +149,8 @@ category('Widgets: Actions', () => {
     await delay(500);
   });
 
+  after(async () => await delay(3000));
+
   test('New view', async () => {
     // Set compound bitset: filter out 2 rows and select 1 among them
     const filter = model.df.filter;

package/src/utils/cell-renderer.ts

@@ -81,12 +81,16 @@ export function renderMutationCliffCell(canvasContext: CanvasRenderingContext2D,
 export function renderInvaraintMapCell(canvasContext: CanvasRenderingContext2D, currentMonomer: string,
   currentPosition: string, invariantMapSelection: types.Selection, cellValue: number, bound: DG.Rect,
   color: number): void {
+  //FIXME: This is a hack, because `color` value sometimes comes incomplete. E.g. we found that here `color` value is
+  // 255 and its contrast color would be black, which is not visible on blue (color code) background. The full number
+  // is actually 4278190335.
+  color = DG.Color.fromHtml(DG.Color.toHtml(color));
   canvasContext.fillStyle = DG.Color.toHtml(color);
   canvasContext.fillRect(bound.x, bound.y, bound.width, bound.height);
   canvasContext.font = '13px Roboto, Roboto Local, sans-serif';
   canvasContext.textAlign = 'center';
   canvasContext.textBaseline = 'middle';
-  canvasContext.fillStyle = '#000';
+  canvasContext.fillStyle = DG.Color.toHtml(DG.Color.getContrastColor(color));
   canvasContext.fillText(cellValue.toString(), bound.x + (bound.width / 2), bound.y + (bound.height / 2), bound.width);
 
   const monomerSelection = invariantMapSelection[currentPosition];
@@ -114,18 +118,19 @@ export function drawLogoInBounds(ctx: CanvasRenderingContext2D, bounds: DG.Rect,
   drawOptions.symbolStyle ??= '16px Roboto, Roboto Local, sans-serif';
   drawOptions.upperLetterHeight ??= 12.2;
   drawOptions.upperLetterAscent ??= 0.25;
-  drawOptions.marginVertical ??= 5;
-  drawOptions.marginHorizontal ??= 5;
+  drawOptions.marginVertical ??= 2;
+  drawOptions.marginHorizontal ??= 2;
+  drawOptions.selectionWidth ??= 1;
   drawOptions.textHeight ??= 13;
   drawOptions.headerStyle ??= `bold ${drawOptions.textHeight * pr}px Roboto, Roboto Local, sans-serif`;
 
   const totalSpace = (sortedOrder.length - 1) * drawOptions.upperLetterAscent; // Total space between letters
   const barHeight = (bounds.height - 2 * drawOptions.marginVertical - totalSpace - 1.25 * drawOptions.textHeight) * pr;
   const leftShift = drawOptions.marginHorizontal * 2;
-  const barWidth = (bounds.width - leftShift * 2) * pr;
+  const barWidth = (bounds.width - (leftShift + drawOptions.marginHorizontal)) * pr;
   const xStart = (bounds.x + leftShift) * pr;
-  const selectionWidth = 4 * pr;
-  const xSelection = (bounds.x + 3) * pr;
+  const selectionWidth = Math.min(drawOptions.selectionWidth * pr, 1);
+  const xSelection = (bounds.x + 1) * pr;
   let currentY = (bounds.y + drawOptions.marginVertical) * pr;
 
   const monomerBounds: { [monomer: string]: DG.Rect } = {};

package/src/utils/constants.ts

@@ -43,6 +43,7 @@ export enum TAGS {
   MULTIPLE_VIEWS = 'isMultipleViews',
   IDENTITY_TEMPLATE = 'Identity template',
   SIMILARITY_TEMPLATE = 'Similarity template',
+  ANALYSIS_COL = 'isAnalysisCol',
 }
 
 export enum SEM_TYPES {

package/src/utils/misc.ts

@@ -36,7 +36,7 @@ export function scaleActivity(activityCol: DG.Column<number>, scaling: C.SCALING
       const val = activityColData[i];
       return val === DG.FLOAT_NULL || val === DG.INT_NULL ? val : formula(val);
     });
-
+  scaledCol.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
   return scaledCol;
 }
 
@@ -131,4 +131,5 @@ export function setGridProps(grid: DG.Grid): void {
   grid.props.showRowHeader = false;
   grid.props.showCurrentRowIndicator = false;
   grid.root.style.width = '100%';
+  grid.root.style.maxWidth = '100%';
 }