@datagrok/peptides 0.8.5 → 0.8.6

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.8.5",
+	"version": "0.8.6",
 	"description": "",
 	"dependencies": {
 		"@biowasm/aioli": ">=2.4.0",
@@ -12,7 +12,7 @@
 		"@types/jquery": "^3.5.6",
 		"cash-dom": "latest",
 		"d3": "latest",
-		"datagrok-api": ">=0.104.0",
+		"datagrok-api": ">=0.115.0",
 		"dayjs": "latest",
 		"file-loader": "^6.2.0",
 		"jstat": "^1.9.5",

package/setup.sh

@@ -0,0 +1,15 @@
+npm unlink datagrok-api
+npm unlink @datagrok-libraries/utils
+npm unlink @datagrok-libraries/ml
+cd ../../js-api
+npm install
+npm link
+cd ../libraries/utils
+npm install
+npm link
+cd ../../libraries/ml
+npm install
+npm link datagrok-api @datagrok-libraries/utils
+cd ../../packages/Peptides
+npm install
+npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/ml 

package/src/describe.ts

@@ -60,41 +60,38 @@ function joinDataFrames(
   splitSeqDf: DG.DataFrame,
   activityColumn: string,
 ) {
-  if (df.col(activityColumnScaled)) {
-    df.columns.remove(activityColumnScaled);
-  }
+  if (df.col(activityColumnScaled))
+  (df.columns as DG.ColumnList).remove(activityColumnScaled);
+
 
   //FIXME: this column usually duplicates, so remove it then
-  if (df.col(`${activityColumnScaled} (2)`)) {
-    df.columns.remove(`${activityColumnScaled} (2)`);
-  }
+  if (df.col(`${activityColumnScaled} (2)`))
+    (df.columns as DG.ColumnList).remove(`${activityColumnScaled} (2)`);
+
 
   // append splitSeqDf columns to source table and make sure columns are not added more than once
   const dfColsSet = new Set(df.columns.names());
-  if (!positionColumns.every((col: string) => dfColsSet.has(col))) {
+  if (!positionColumns.every((col: string) => dfColsSet.has(col)))
     df.join(splitSeqDf, [activityColumn], [activityColumn], df.columns.names(), positionColumns, 'inner', true);
-  }
 }
 
 function sortSourceGrid(sourceGrid: DG.Grid) {
   if (sourceGrid) {
-    const colNames:string[] = [];
-    for (let i = 0; i < sourceGrid.columns.length; i++) {
-      colNames.push(sourceGrid.columns.byIndex(i)!.name);
-    }
+    const colNames: DG.GridColumn[] = [];
+    for (let i = 1; i < sourceGrid.columns.length; i++)
+      colNames.push(sourceGrid.columns.byIndex(i)!);
+
     colNames.sort((a, b)=>{
-      if (sourceGrid.columns.byName(a)?.column?.semType == 'aminoAcids') {
-        if (sourceGrid.columns.byName(b)?.column?.semType == 'aminoAcids') {
+      if (a.column!.semType == 'aminoAcids') {
+        if (b.column!.semType == 'aminoAcids')
           return 0;
-        }
         return -1;
       }
-      if (sourceGrid.columns.byName(b)?.column?.semType == 'aminoAcids') {
+      if (b.column!.semType == 'aminoAcids')
         return 1;
-      }
       return 0;
     });
-    sourceGrid?.columns.setOrder(colNames);
+    sourceGrid.columns.setOrder(colNames.map((v) => v.name));
   }
 }
 
@@ -180,13 +177,13 @@ async function calculateStatistics(
     pvalues[i] = pvalue;
   }
 
-  if (true) {
+  if (true)
     pvalues = fdrcorrection(pvalues)[1];
-  }
 
-  for (let i = 0; i < pvalues.length; ++i) {
+
+  for (let i = 0; i < pvalues.length; ++i)
     pValCol.set(i, pvalues[i]);
-  }
+
 
   return matrixDf.clone();
 }
@@ -195,9 +192,9 @@ async function setCategoryOrder(
   twoColorMode: boolean, statsDf: DG.DataFrame, aminoAcidResidue: string, matrixDf: DG.DataFrame,
 ) {
   const sortArgument = twoColorMode ? 'Absolute Mean difference' : 'Mean difference';
-  if (twoColorMode) {
+  if (twoColorMode)
     await statsDf.columns.addNewCalculated('Absolute Mean difference', 'Abs(${Mean difference})');
-  }
+
   const aarWeightsDf = statsDf.groupBy([aminoAcidResidue]).sum(sortArgument, 'weight').aggregate();
   const aarList = aarWeightsDf.getCol(aminoAcidResidue).toList();
   const getWeight = (aar: string) => aarWeightsDf
@@ -257,13 +254,12 @@ function createGrids(
 
   if (!grouping) {
     let tempCol = matrixDf.columns.byName(aminoAcidResidue);
-    if (tempCol) {
+    if (tempCol)
       setAARRenderer(tempCol, sarGrid);
-    }
+
     tempCol = sequenceDf.columns.byName(aminoAcidResidue);
-    if (tempCol) {
+    if (tempCol)
       setAARRenderer(tempCol, sarGrid);
-    }
   }
 
   return [sarGrid, sarVGrid];
@@ -308,15 +304,15 @@ function setCellRendererFunc(
 
         let coef;
         const variant = args.cell.cell.value < 0;
-        if (pVal < 0.01) {
+        if (pVal < 0.01)
           coef = variant && twoColorMode ? '#FF7900' : '#299617';
-        } else if (pVal < 0.05) {
+        else if (pVal < 0.05)
           coef = variant && twoColorMode ? '#FFA500' : '#32CD32';
-        } else if (pVal < 0.1) {
+        else if (pVal < 0.1)
           coef = variant && twoColorMode ? '#FBCEB1' : '#98FF98';
-        } else {
+        else
           coef = DG.Color.toHtml(DG.Color.lightLightGray);
-        }
+
 
         const chooseMin = () => twoColorMode ? 0 : mdCol.min;
         const chooseMax = () => twoColorMode ? Math.max(Math.abs(mdCol.min), mdCol.max) : mdCol.max;
@@ -380,11 +376,11 @@ function setTooltipFunc(
           const textNum = statsDf.groupBy([col]).where(query).aggregate().get(col, 0);
           let text = `${col === 'Count' ? textNum : textNum.toFixed(5)}`;
 
-          if (col === 'Count') {
+          if (col === 'Count')
             text += ` / ${peptidesCount}`;
-          } else if (col === 'pValue') {
+          else if (col === 'pValue')
             text = parseFloat(text) !== 0 ? text : '<0.01';
-          }
+
 
           tooltipMap[col === 'pValue' ? 'p-value' : col] = text;
         }
@@ -403,9 +399,8 @@ function setTooltipFunc(
         const currentGroup = groupDescription[cell.cell.value];
         const divText = ui.divText('Amino Acids in this group: ' + currentGroup['aminoAcids'].join(', '));
         ui.tooltip.show(ui.divV([ui.h3(currentGroup['description']), divText]), x, y);
-      } else {
+      } else
         cp.showTooltip(cell, x, y);
-      }
     }
     return true;
   };
@@ -424,14 +419,13 @@ function postProcessGrids(
 ) {
   sourceGrid.onCellPrepare((cell: DG.GridCell) => {
     const currentRowIndex = cell.tableRowIndex;
-    if (currentRowIndex && invalidIndexes.includes(currentRowIndex) && !cell.isRowHeader) {
+    if (currentRowIndex && invalidIndexes.includes(currentRowIndex) && !cell.isRowHeader)
       cell.style.backColor = DG.Color.lightLightGray;
-    }
   });
 
-  for (const col of matrixDf.columns.names()) {
+  for (const col of matrixDf.columns.names())
     sarGrid.col(col)!.width = sarGrid.props.rowHeight;
-  }
+
 
   if (grouping) {
     sarGrid.col(aminoAcidResidue)!.name = 'Groups';
@@ -440,6 +434,8 @@ function postProcessGrids(
 
   sarGrid.props.allowEdit = false;
   sarVGrid.props.allowEdit = false;
+
+  sarVGrid.col('Mean difference')!.name = 'Diff';
 }
 
 export async function describe(
@@ -469,9 +465,8 @@ export async function describe(
   joinDataFrames(activityColumnScaled, df, positionColumns, splitSeqDf, activityColumn);
 
   for (const col of df.columns) {
-    if (splitSeqDf.col(col.name) && col.name != activityColumn) {
+    if (splitSeqDf.col(col.name) && col.name != activityColumn)
       setAARRenderer(col, sourceGrid);
-    }
   }
 
   sortSourceGrid(sourceGrid);
@@ -495,9 +490,9 @@ export async function describe(
     const aarCol = matrixDf.getCol(aminoAcidResidue);
     aarCol.init((index) => groupMapping[aarCol.get(index)[0]] ?? '-');
     aarCol.compact();
-  } else {
+  } else
     Object.keys(aarGroups).forEach((value) => groupMapping[value] = value);
-  }
+
 
   //statistics for specific AAR at a specific position
   const statsDf = await calculateStatistics(

package/src/monomer-library.ts

@@ -0,0 +1,187 @@
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+/** HELM associated sdf libraries with monomer processing*/
+export class MonomerLibrary {
+  private monomerFields: string[] = ['molecule', 'MonomerType', 'MonomerNaturalAnalogCode', 'MonomerName', 'MonomerCode', 'MonomerCaps', 'BranchMonomer'];
+  private library: {
+    [name: string]: {
+      mol: string,
+      type: string,
+      analogueCode: string,
+      linkages: { [link: string]: { atomNumber: number, type: string } }
+    }
+  } = {};
+  private monomers: string[] = [];
+
+  constructor(sdf: string) {
+    //sdf = sdf.replaceAll('\n\[', '\[');
+    const sdfReader = new SDFReader();
+    const data = sdfReader.get_colls(sdf);
+    this.monomerFields.forEach((f) => {
+      if (!(f in data))
+        throw `Monomer library was not compiled: ${f} field is absent in provided file`;
+
+      if (data[f].length != data.molecule.length)
+        throw `Monomer library was not compiled: ${f} field is not presented for each monomer`;
+    });
+
+    for (let i = 0; i < data.molecule.length; i++) {
+      const linkData = this.getLinkData(data.molecule[i], data.MonomerCaps[i], data.MonomerName[i]);
+      const entry = {
+        mol: data.molecule[i],
+        type: 'Peptide',
+        code: data.MonomerCode[i],
+        analogueCode: data.MonomerNaturalAnalogCode[i],
+        linkages: linkData,
+      };
+
+      const name = data.MonomerCode[i] !== '.' ? data.MonomerCode[i] : data.MonomerName[i];
+      this.library[name] = entry;
+      this.monomers.push(data.MonomerName[i]);
+    }
+  }
+
+  /** getting full monomer information from monomer library*/
+  public getMonomerEntry(name: string) {
+    if (!this.monomers.includes(name))
+      throw `Monomer library do not contain ${name} monomer`;
+
+
+    return this.library[name];
+  }
+
+  /** getting mol as string for monomer*/
+  public getMonomerMol(name: string) {
+    if (!this.monomers.includes(name))
+      throw `Monomer library do not contain ${name} monomer`;
+
+
+    const entry = this.library[name];
+    let monomerMol = entry.mol.replace(/M  RGP  .+\n/, '');
+
+    //order matters
+    const links = Object.keys(entry.linkages);
+    for (let i = 0; i < links.length; i++)
+      monomerMol = monomerMol.replace('R#', entry.linkages[links[i]].type + ' ');
+
+
+    return monomerMol;
+  }
+
+  /** getting the list of the minomers available in library*/
+  get monomerNames() {
+    return this.monomers;
+  }
+
+  private getLinkData(mol: string, caps: string, name: string) {
+    const rawData = mol.match(/M  RGP  .+/);
+    if (rawData === null)
+      throw `Monomer library was not compiled: ${name} entry has no RGP`;
+
+
+    const types: { [code: string]: string } = {};
+    caps.split('\n')?.forEach((e) => {
+      types[e.match(/\d+/)![0]] = e.match(/(?<=\])\w+/)![0];
+    });
+
+    const data = rawData![0].replace('M  RGP  ', '').split(/\s+/);
+    const res: { [link: string]: { atomNumber: number, type: string } } = {};
+    for (let i = 0; i < parseInt(data[0]); i++) {
+      const code = parseInt(data[2 * i + 2]);
+      let type = '';
+      switch (code) {
+      case 1:
+        type = 'N-terminal';
+        break;
+      case 2:
+        type = 'C-terminal';
+        break;
+      case 3:
+        type = 'branch';
+        break;
+      default:
+        break;
+      }
+      res[type] = {atomNumber: parseInt(data[2 * i + 1]), type: types[code]};
+    }
+
+    return res;
+  }
+}
+
+//TODO: merge with Chem version
+class SDFReader {
+  dataColls: { [_: string]: any };
+
+  constructor() {
+    this.dataColls = {'molecule': []};
+  }
+
+  get_colls(content: string) {
+    this.read(content);
+    return this.dataColls;
+  }
+
+  read(content: string) {
+    content = content.replaceAll('\r', ''); //equalize old and new sdf standards
+    let startIndex = content.indexOf('$$$$', 0);
+    this.parse(content, 0, startIndex, (name: string, val: any) => { // TODO: type
+      this.dataColls[name] = [];
+      this.dataColls[name].push(val);
+    });
+    startIndex += 5;
+    while (startIndex > -1 && startIndex < content.length)
+      startIndex = this.readNext(content, startIndex);
+  }
+
+  readNext(content: string, startIndex: number) {
+    const nextStartIndex = content.indexOf('$$$$', startIndex);
+    if (nextStartIndex === -1)
+      return -1;
+    else {
+      this.parse(content, startIndex, nextStartIndex,
+        (name: string, val: number) => this.dataColls[name].push(val));
+    }
+
+    if (nextStartIndex > -1)
+      return nextStartIndex + 5;
+
+
+    return nextStartIndex;
+  }
+
+  parse(content: string, start: number, end: number, handler: any) {
+    const molEnd = +content.indexOf('M  END\n', start) + 7;
+    let localEnd = start;
+    this.dataColls['molecule'].push(content.substr(start, molEnd - start));
+
+    start = molEnd;
+    while (localEnd < end) {
+      start = content.indexOf('> <', localEnd);
+      if (start === -1)
+        return;
+
+
+      start += 3;
+      localEnd = content.indexOf('>\n', start);
+      if (localEnd === -1)
+        return;
+
+
+      const propertyName = content.substring(start, localEnd);
+      start = localEnd + 2;
+
+      localEnd = content.indexOf('\n', start);
+      if (localEnd === -1)
+        localEnd = end;
+      else if (content[localEnd + 1] != '\n')
+        localEnd = content.indexOf('\n', ++localEnd);
+      ;
+
+      handler(propertyName, content.substring(start, localEnd));
+      localEnd += 2;
+    }
+  }
+}

package/src/package.ts

@@ -38,9 +38,9 @@ async function main(chosenFile: string) {
   pi.close();
 }
 
-//name: Peptides App
+//name: Peptides
 //tags: app
-export function Peptides() {
+export async function Peptides() {
   const wikiLink = ui.link('wiki', 'https://github.com/datagrok-ai/public/blob/master/help/domains/bio/peptides.md');
   const textLink = ui.inlineText(['For more details, see our ', wikiLink, '.']);
 
@@ -73,8 +73,8 @@ export function Peptides() {
     appDescription,
     ui.info([textLink]),
     ui.divH([
-      ui.button('Open peptide sequences demonstration set', () => main('aligned.csv'), ''),
-      ui.button('Open complex case demo', () => main('aligned_2.csv'), ''),
+      ui.button('Simple demo', () => main('aligned.csv'), ''),
+      ui.button('Complex demo', () => main('aligned_2.csv'), ''),
     ]),
   ]);
 }
@@ -84,9 +84,9 @@ export function Peptides() {
 //input: column col {semType: alignedSequence}
 //output: widget result
 export async function peptidesPanel(col: DG.Column): Promise<DG.Widget> {
-  if (col.getTag('isAnalysisApplicable') === 'false') {
+  if (col.getTag('isAnalysisApplicable') === 'false')
     return new DG.Widget(ui.divText('Analysis is not applicable'));
-  }
+
   view = (grok.shell.v as DG.TableView);
   tableGrid = view.grid;
   currentDf = col.dataFrame;
@@ -136,6 +136,15 @@ export async function peptideMolecule(peptide: string): Promise<DG.Widget> {
   return await peptideMoleculeWidget(peptide);
 }
 
+//name: Peptide Molecule
+//tags: panel, widgets
+//input: string aar {semType: aminoAcids}
+//output: widget result
+export async function peptideMolecule2(aar: string): Promise<DG.Widget> {
+  const peptide = alignedSequenceCol.get(currentDf.currentRowIdx);
+  return await peptideMolecule(peptide);
+}
+
 //name: StackedBarChartAA
 //tags: viewer
 //output: viewer result
@@ -171,6 +180,7 @@ export function logov() {
 //input: string monomer {semType: aminoAcids}
 //output: widget result
 export function manualAlignment(monomer: string) {
+  //TODO: recalculate Molfile and Molecule panels on sequence update
   return manualAlignmentWidget(alignedSequenceCol, currentDf);
 }
 
@@ -192,6 +202,15 @@ export async function peptideMolfile(peptide: string): Promise<DG.Widget> {
   return await grok.functions.call('Chem:molfile', {'smiles': smiles});
 }
 
+//name: Molfile
+//tags: panel, widgets
+//input: string aar { semType: aminoAcids }
+//output: widget result
+export async function peptideMolfile2(aar: string): Promise<DG.Widget> {
+  const peptide = alignedSequenceCol.get(currentDf.currentRowIdx);
+  return await peptideMolfile(peptide);
+}
+
 //name: Multiple sequence alignment
 //tags: panel
 //input: column col {semType: alignedSequence}

package/src/peptides.ts

@@ -59,10 +59,14 @@ export class Peptides {
     // const layout1 = view.saveLayout();
     // view.dockManager.close(substNode);
 
+    const helpUrl = '/help/domains/bio/peptides.md';
+
     const sarViewer = view.addViewer('peptide-sar-viewer', options);
+    sarViewer.helpUrl = helpUrl;
     const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
 
     const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
+    sarViewerVertical.helpUrl = helpUrl;
     const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
 
     const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
@@ -87,17 +91,15 @@ export class Peptides {
     const hideIcon = ui.iconFA('window-close', () => { //undo?, times?
       const viewers = [];
       for (const viewer of view.viewers) {
-        if (viewer.type !== DG.VIEWER.GRID) {
+        if (viewer.type !== DG.VIEWER.GRID)
           viewers.push(viewer);
-        }
       }
       viewers.forEach((v) => v.close());
 
       const cols = (currentDf.columns as DG.ColumnList);
       for (const colName of cols.names()) {
-        if (!originalDfColumns.includes(colName)) {
+        if (!originalDfColumns.includes(colName))
           cols.remove(colName);
-        }
       }
 
       currentDf.selection.setAll(false);
@@ -132,9 +134,11 @@ export class Peptides {
       nodeList.length = 0;
       if (isSA) {
         const sarViewer = view.addViewer('peptide-sar-viewer', options);
+        sarViewer.helpUrl = helpUrl;
         const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
 
         const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
+        sarViewerVertical.helpUrl = helpUrl;
         const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
 
         const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
@@ -152,7 +156,8 @@ export class Peptides {
         const substViewer = view.addViewer(
           'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
         );
-        nodeList.push(view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis'));
+        substViewer.helpUrl = helpUrl;
+        nodeList.push(view.dockManager.dock(substViewer, DG.DOCK_TYPE.DOWN, null, 'Substitution Analysis'));
         $(switchViewers).removeClass('fa-toggle-on');
         $(switchViewers).addClass('fa-toggle-off');
       }

package/src/tests/peptides-tests.ts

@@ -1,15 +1,15 @@
-import {after, before, category, expect, test} from "@datagrok-libraries/utils/src/test";
-import {splitAlignedPeptides} from "../utils/split-aligned";
-import * as DG from "datagrok-api/dg";
-import * as grok from "datagrok-api/grok";
-import * as ui from "datagrok-api/ui";
-import { Peptides } from "../peptides";
-import { describe } from "../describe";
-import { analyzePeptidesWidget } from "../widgets/analyze-peptides";
-import { manualAlignmentWidget } from "../widgets/manual-alignment";
-import { peptideMoleculeWidget } from "../widgets/peptide-molecule";
-
-export let _package = new DG.Package();
+import {after, before, category, test} from '@datagrok-libraries/utils/src/test';
+import {splitAlignedPeptides} from '../utils/split-aligned';
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+import {Peptides} from '../peptides';
+import {describe} from '../describe';
+import {analyzePeptidesWidget} from '../widgets/analyze-peptides';
+import {manualAlignmentWidget} from '../widgets/manual-alignment';
+import {peptideMoleculeWidget} from '../widgets/peptide-molecule';
+import * as P from '../package';
+
+// let _package = new DG.Package();
 
 category('peptides', async () => {
   let peptidesDf: DG.DataFrame;
@@ -19,7 +19,7 @@ category('peptides', async () => {
   let pepView: DG.TableView;
 
   before(async () => {
-    // peptidesDf = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
+    // peptidesDf = DG.DataFrame.fromCsv(await P._package.files.readAsText('aligned.csv'));
     const csv = `ID,AlignedSequence,IC50
     1,NH2--A-Q-T-T-Y-K-N-Y-R-R-N-L-L--COOH,4.6411368455908086e-4
     2,NH2-M-A-N-T-T-Y-K-N-Y-R-N-N-L-L--COOH,0.003327324930165897
@@ -45,9 +45,9 @@ category('peptides', async () => {
       'activityColumnName': 'IC50',
       'scaling': '-lg',
     };
-    peptidesGrid = peptidesDf.plot.grid();
     asCol = peptidesDf.getCol('AlignedSequence');
     pepView = grok.shell.addTableView(peptidesDf);
+    peptidesGrid = pepView.grid;
   });
 
   test('utils.split-sequence', async () => {
@@ -56,7 +56,7 @@ category('peptides', async () => {
 
   test('describe', async () => {
     await describe(
-      peptidesDf, options['activityColumnName'], options['scaling'],  peptidesGrid, true,
+      peptidesDf, options['activityColumnName'], options['scaling'], peptidesGrid, true,
       DG.BitSet.create(peptidesDf.rowCount, (i) => i % 2 === 0), true);
   });
 
@@ -65,6 +65,10 @@ category('peptides', async () => {
     peptides.init(peptidesGrid, pepView, peptidesDf, options, asCol);
   });
 
+  test('panel.peptides', async () => {
+    await P.peptidesPanel(asCol);
+  });
+
   test('widgets.analyze-peptides', async () => {
     await analyzePeptidesWidget(asCol, pepView, peptidesGrid, peptidesDf);
   });
@@ -77,8 +81,40 @@ category('peptides', async () => {
     await peptideMoleculeWidget('NH2--A-N-T-T-Y-K-N-Y-R-S-N-L-L--COOH');
   });
 
+  test('widgets.molfile', async () => {
+    await P.peptideMolfile2('');
+  });
+
+  test('renderers.aligned-sequence-cell', async () => {
+    P.alignedSequenceCellRenderer();
+  });
+
+  test('renderers.amino-acids-cell', async () => {
+    P.aminoAcidsCellRenderer();
+  });
+
+  test('viewers.logo-viewer', async () => {
+    P.logov();
+  });
+
+  test('viewers.sar-viewer', async () => {
+    P.sar();
+  });
+
+  test('viewers.sar-vertical-viewer', async () => {
+    P.sarVertical();
+  });
+
+  test('viewers.stacked-barchart-viewer', async () => {
+    P.stackedBarChart();
+  });
+
+  test('viewers.subst-viewer', async () => {
+    P.subst();
+  });
+
   after(async () => {
     pepView.close();
     grok.shell.closeTable(peptidesDf);
-  })
+  });
 });

package/src/tests/utils.ts

@@ -77,9 +77,8 @@ export async function _testPeptideSimilaritySpaceViewer(
     const axesNames = ['~X', '~Y', '~MW'];
     const axes = axesNames.map((v) => df?.getCol(v).getRawData() as Float32Array);
 
-    for (const ax of axes) {
+    for (const ax of axes)
       expect(ax.every((v) => v !== null && v !== NaN), true);
-    }
   } catch (error) {
     noException = false;
   }