@datagrok/bio 2.10.27 → 2.10.28

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.10.27",
+  "version": "2.10.28",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -36,7 +36,7 @@
     "@biowasm/aioli": "^3.1.0",
     "@datagrok-libraries/bio": "^5.38.13",
     "@datagrok-libraries/chem-meta": "^1.0.1",
-    "@datagrok-libraries/ml": "^6.3.49",
+    "@datagrok-libraries/ml": "^6.3.50",
     "@datagrok-libraries/tutorials": "^1.3.6",
     "@datagrok-libraries/utils": "^4.0.17",
     "cash-dom": "^8.0.0",
@@ -101,5 +101,36 @@
   "sources": [
     "css/helm.css"
   ],
-  "category": "Bioinformatics"
+  "category": "Bioinformatics",
+  "meta": {
+    "menu": {
+      "Bio": {
+        "Analyze": {
+          "SAR...": null,
+          "Sequence Space...": null,
+          "Hierarchical Clustering...": null,
+          "Activity Cliffs...": null,
+          "Sequence Space": null,
+          "MSA...": null,
+          "Composition": null
+        },
+        "Search": {
+          "Diversity Search": null,
+          "Similarity Search": null,
+          "Subsequence Search...": null
+        },
+        "Calculate": {
+          "Identity...": null,
+          "Similarity...": null
+        },
+        "Convert": {
+          "Split to Monomerts...": null,
+          "Get Region...": null,
+          "Notation...": null,
+          "SDF to JSON Library...": null,
+          "To Atomic Level...": null
+        }
+      }
+    }
+  }
 }

package/src/package.ts

@@ -74,6 +74,7 @@ import {DIMENSIONALITY_REDUCER_TERMINATE_EVENT}
   from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
 import {sequenceToMolfile} from './utils/sequence-to-mol';
+import {SHOW_SCATTERPLOT_PROGRESS} from '@datagrok-libraries/ml/src/functionEditors/seq-space-base-editor';
 
 export const _package = new BioPackage();
 
@@ -465,7 +466,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
 //input: string methodName { choices:["UMAP", "t-SNE"] }
 //input: string similarityMetric { choices:["Hamming", "Levenshtein", "Monomer chemical distance"] }
 //input: bool plotEmbeddings = true
-//input: double sparseMatrixThreshold = 0.8 [Similarity Threshold for sparse matrix calculation]
+//input: double sparseMatrixThreshold = 0 [Similarity Threshold for sparse matrix calculation]
 //input: object options {optional: true}
 //output: viewer result
 //editor: Bio:SequenceSpaceEditor
@@ -498,8 +499,11 @@ export async function sequenceSpaceTopMenu(
         embedYCol = table.columns.byName(embedColsNames[1]);
       }
 
-      embedXCol.init((i) => embeddings[i] ? embeddings[i][0] : undefined);
-      embedYCol.init((i) => embeddings[i] ? embeddings[i][1] : undefined);
+      if (options?.[SHOW_SCATTERPLOT_PROGRESS]) {
+        scatterPlot?.root && ui.setUpdateIndicator(scatterPlot!.root, false);
+        embedXCol.init((i) => embeddings[i] ? embeddings[i][0] : undefined);
+        embedYCol.init((i) => embeddings[i] ? embeddings[i][1] : undefined);
+      }
       const progress = (_nEpoch / epochsLength * 100);
       pg.update(progress, `Running sequence space ... ${progress.toFixed(0)}%`);
     }
@@ -525,6 +529,14 @@ export async function sequenceSpaceTopMenu(
     }
 
     async function getSeqSpace() {
+      table.columns.add(DG.Column.float(embedColsNames[0], table.rowCount));
+      table.columns.add(DG.Column.float(embedColsNames[1], table.rowCount));
+      if (plotEmbeddings) {
+        scatterPlot = grok.shell
+          .tableView(table.name)
+          .scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
+        ui.setUpdateIndicator(scatterPlot.root, true);
+      }
       let resolveF: Function | null = null;
 
       const sub = grok.events.onViewerClosed.subscribe((args) => {
@@ -580,6 +592,7 @@ export async function sequenceSpaceTopMenu(
             .tableView(table.name)
             .scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
         }
+        ui.setUpdateIndicator(scatterPlot.root, false);
         return scatterPlot;
       }
     }

package/src/tests/WebLogo-positions-test.ts

@@ -32,7 +32,7 @@ ATC-G-TTGC--
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 300);
+    }, 500);
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -122,7 +122,7 @@ ATC-G-TTGC--
       {'skipEmptyPositions': true})) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 300);
+    }, 500);
     const resPosList: PI[] = wlViewer['positions'];
 
     const tgtPosList: PI[] = [
@@ -158,7 +158,7 @@ ATC-G-TTGC--
     })) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 300);
+    }, 500);
     const resPosList: PI[] = wlViewer['positions'];
     const tgtPosList: PI[] = [
       new PI(2, '3', {'C': new PMI(5)}),
@@ -194,7 +194,7 @@ ATC-G-TTGC--
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 300);
+    }, 500);
     const resPosList: PI[] = wlViewer['positions'];
   });
 });