@datagrok/peptides 1.3.7 → 1.3.8

package/src/widgets/peptides.ts

@@ -14,28 +14,40 @@ import {scaleActivity} from '../utils/misc';
  * @param {DG.DataFrame} df Working table
  * @param {DG.Column} col Aligned sequence column
  * @return {Promise<DG.Widget>} Widget containing peptide analysis */
-export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): Promise<DG.Widget> {
-  if (!col.tags['aligned']?.includes('MSA') && col.tags[DG.TAGS.UNITS].toLowerCase() != 'helm')
-    return new DG.Widget(ui.divText('Peptides analysis only works with aligned sequences'));
+export async function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
+Promise<{host: HTMLElement, callback: () => Promise<void>}> {
+  let seqColInput: DG.InputBase | null = null;
+  if (typeof col === 'undefined') {
+    const sequenceColumns = df.columns.toList().filter((dfCol) => dfCol.semType === DG.SEMTYPE.MACROMOLECULE);
+    let potentialCol = DG.Utils.firstOrNull(sequenceColumns);
+    if (potentialCol === null)
+      throw new Error('Peptides Error: table doesn\'t contain sequence columns');
+    seqColInput = ui.columnInput('Sequence', df, potentialCol, () => {
+      const seqCol = seqColInput!.value;
+      if (!seqCol.tags['aligned']?.includes('MSA') && seqCol.tags[DG.TAGS.UNITS].toLowerCase() !== 'helm')
+        grok.shell.warning('Peptides analysis only works with aligned sequences');
+    });
+  } else if (!col.tags['aligned']?.includes('MSA') && col.tags[DG.TAGS.UNITS].toLowerCase() !== 'helm')
+    return {host: ui.label('Peptides analysis only works with aligned sequences'), callback: async () => {}};
 
   let funcs = DG.Func.find({package: 'Bio', name: 'webLogoViewer'});
   if (funcs.length == 0)
-    return new DG.Widget(ui.label('Bio package is missing or out of date. Please install the latest version.'));
+    return {host: ui.label('Bio package is missing or out of date. Please install the latest version.'), callback: async () => {}};
 
-  funcs = DG.Func.find({package: 'Helm', name: 'getMonomerLib'});
+  funcs = DG.Func.find({package: 'Bio', name: 'getBioLib'});
   if (funcs.length == 0)
-    return new DG.Widget(ui.label('Helm package is missing or out of date. Please install the latest version.'));
+    return {host: ui.label('Bio package is missing or out of date. Please install the latest version.'), callback: async () => {}};
 
   let scaledCol: DG.Column<number>;
 
   const defaultActivityColumn: DG.Column<number> | null =
-    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical);;
+    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical); ;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
   const activityScalingMethod = ui.choiceInput(
     'Scaling', 'none', ['none', 'lg', '-lg'],
     async (currentMethod: string): Promise<void> => {
-      scaledCol = scaleActivity(currentMethod, activityColumnChoice.value!);
+      scaledCol = scaleActivity(activityColumnChoice.value!, currentMethod);
 
       const hist = DG.DataFrame.fromColumns([scaledCol]).plot.histogram({
         filteringEnabled: false,
@@ -62,37 +74,48 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   activityScalingMethod.fireChanged();
 
   const inputsList = [activityColumnChoice, activityScalingMethod, clustersColumnChoice];
+  if (seqColInput !== null)
+    inputsList.splice(0, 0, seqColInput);
 
   const bitsetChanged = df.filter.onChanged.subscribe(() => {
     activityScalingMethodState();
-  })
+  });
 
-  const startBtn = ui.button('Launch SAR', async () => {
-    await startAnalysis(activityColumnChoice.value!, col, clustersColumnChoice.value, df, scaledCol,
-      activityScalingMethod.value ?? 'none');
+  const startAnalysisCallback = async () => {
+    const sequencesCol = col ?? seqColInput!.value;
+    if (sequencesCol)
+      await startAnalysis(activityColumnChoice.value!, sequencesCol, clustersColumnChoice.value, df, scaledCol,
+        activityScalingMethod.value ?? 'none');
     bitsetChanged.unsubscribe();
-  });
-  startBtn.style.alignSelf = 'center';
+  };
+
+  const inputElements: HTMLElement[] = [ui.inputs(inputsList)];
+  $(inputElements[0]).find('label').css('width', 'unset');
+  if (typeof col !== 'undefined') {
+    const startBtn = ui.button('Launch SAR', startAnalysisCallback);
+    startBtn.style.alignSelf = 'center';
+    inputElements.push(startBtn);
+  }
 
   const viewer = await df.plot.fromType('WebLogo') as bio.WebLogoViewer;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
 
-  return new DG.Widget(
-    ui.divV([
-      logoHost,
-      ui.splitH([
-        ui.splitV([ui.inputs(inputsList), startBtn]),
-        histogramHost,
-      ], {style: {height: '215px'}}),
-    ]),
-  );
+  const mainHost = ui.divV([
+    logoHost,
+    ui.splitH([
+      ui.splitV(inputElements),
+      histogramHost,
+    ], {style: {height: '215px'}}),
+  ]);
+  mainHost.style.maxWidth = '400px';
+  return {host: mainHost, callback: startAnalysisCallback};
 }
 
 export async function startAnalysis(activityColumn: DG.Column<number>, peptidesCol: DG.Column<string>,
   clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaledCol: DG.Column<number>, scaling: string,
-  ): Promise<PeptidesModel | null> {
+): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
   if (activityColumn.type === DG.TYPE.FLOAT || activityColumn.type === DG.TYPE.INT) {
@@ -112,9 +135,9 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     newDf.name = 'Peptides analysis';
     if (clustersColumn) {
       newDf.getCol(clustersColumn.name).name = C.COLUMNS_NAMES.CLUSTERS;
-      newDf.tags[C.TAGS.CLUSTERS] = C.COLUMNS_NAMES.CLUSTERS;
+      newDf.setTag(C.TAGS.CLUSTERS, C.COLUMNS_NAMES.CLUSTERS);
     }
-    newDf.tags['scaling'] = scaling;
+    newDf.setTag('settings', JSON.stringify({scaling: scaling}));
 
     let monomerType = 'HELM_AA';
     if (peptidesCol.getTag(DG.TAGS.UNITS).toLowerCase() == 'helm') {

package/src/widgets/settings.ts

@@ -0,0 +1,37 @@
+import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+
+import * as type from '../utils/types';
+import {PeptidesModel} from '../model';
+
+//TODO: show sliderInput values
+export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
+  const settings = model.settings;
+  const result: type.PeptidesSettings = {};
+  const activityScaling = ui.choiceInput('Activity scaling', settings.scaling ?? 'none', ['none', 'lg', '-lg'],
+    () => result.scaling = activityScaling.value! as type.ScalingMethods);
+  const bidirectionalAnalysis = ui.boolInput('Bidirectional analysis', settings.isBidirectional ?? false,
+    () => result.isBidirectional = bidirectionalAnalysis.value!);
+  const maxMutations = ui.sliderInput('Max mutations', settings.maxMutations ?? 1, 0, 50, () => {
+    const val = Math.round(maxMutations.value!);
+    result.maxMutations = val;
+  });
+  const minActivityDelta = ui.sliderInput('Min activity delta', settings.minActivityDelta ?? 0, 0, 100, () => {
+    const val = Math.round(minActivityDelta.value!);
+    result.minActivityDelta = val;
+  });
+
+  const accordion = ui.accordion();
+  accordion.addPane('General', () => ui.inputs([activityScaling, bidirectionalAnalysis]), true);
+  accordion.addPane('Mutation Cliffs', () => ui.inputs([maxMutations, minActivityDelta]), true);
+
+  const dialog = ui.dialog('Peptides settings').add(accordion);
+  dialog.root.style.width = '400px';
+  dialog.onOK(() => model.settings = result);
+  dialog.show();
+
+  return dialog.show();
+}
+
+