Merge branch 'ui-v2' of github.com:IGS/gEAR into ui-v2

www/api/resources/tsne_data.py

@@ -306,13 +306,6 @@ def post(self, dataset_id):
                 if flip_y:
                     adata.obsm[key][:,1] = -1 * adata.obsm[key][:,1]
 
-        # We also need to change the adata's Raw var dataframe
-        # We can't explicitly reset its index so we reinitialize it with
-        # the newer adata object.
-        # https://github.com/theislab/anndata/blob/master/anndata/base.py#L1020-L1022
-        if adata.raw is not None:
-            adata.raw = adata
-
         # Reorder the categorical values in the observation dataframe
         # Currently in UI only "plot_by_group" has reordering capabilities
         if order:

www/js/classes/analysis.js

@@ -1811,6 +1811,8 @@ class AnalysisSteptSNE {
             this.tsneCalculated = Boolean(computeTsne);
             this.umapCalculated = Boolean(computeUmap);
             this.genesToColor = document.querySelector(UI.tsneGenesToColorElt).value;
+            this.nNeighbors = document.querySelector(UI.dimReductionNNeighborsElt).value;
+            this.nPcs = document.querySelector(UI.tsneNPcsElt).value;
             this.plotTsne = plotTsne;
             this.plotUmap = plotUmap;
             this.updateUIWithResults();

www/js/curator_common.js

@@ -490,7 +490,7 @@ const analysisSelectUpdate = async () => {
  */
 const chooseAnalysis = async () => {
     const analysisValue = analysisSelect.selectedOptions.length ? getSelect2Value(analysisSelect) : undefined;
-    const analysisId = (analysisValue && analysisValue > 0) ? analysisValue : null;
+    const analysisId = analysisValue || null;
     const analysisText = (analysisId?.length) ? analysisId : "Primary Analysis";
 
     // Display current selected analysis