Deploying to gh-pages from @ e065626 🚀

Author: rcannood

pkgdown.yml

@@ -8,7 +8,7 @@ articles:
   usage_python: usage_python.html
   usage_seurat: usage_seurat.html
   usage_singlecellexperiment: usage_singlecellexperiment.html
-last_built: 2026-02-26T21:46Z
+last_built: 2026-02-26T21:51Z
 urls:
   reference: https://anndataR.scverse.org/reference
   article: https://anndataR.scverse.org/articles

reference/as_AnnData.html

@@ -330,10 +330,10 @@ obj <- RunUMAP(obj, dims = 1:10)
 #> Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
 #> To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
 #> This message will be shown once per session
-#> 21:46:52 UMAP embedding parameters a = 0.9922 b = 1.112
-#> 21:46:52 Read 200 rows and found 10 numeric columns
-#> 21:46:52 Using Annoy for neighbor search, n_neighbors = 30
-#> 21:46:52 Building Annoy index with metric = cosine, n_trees = 50
+#> 21:51:43 UMAP embedding parameters a = 0.9922 b = 1.112
+#> 21:51:43 Read 200 rows and found 10 numeric columns
+#> 21:51:43 Using Annoy for neighbor search, n_neighbors = 30
+#> 21:51:43 Building Annoy index with metric = cosine, n_trees = 50
 #> 0%   10   20   30   40   50   60   70   80   90   100%
 #> [----|----|----|----|----|----|----|----|----|----|
 #> *
@@ -387,15 +387,15 @@ obj <- RunUMAP(obj, dims = 1:10)
 #> *
 #> *
 #> |
-#> 21:46:52 Writing NN index file to temp file /tmp/RtmpgMQ7R9/file1cb74f681c38
-#> 21:46:52 Searching Annoy index using 1 thread, search_k = 3000
-#> 21:46:52 Annoy recall = 100%
-#> 21:46:53 Commencing smooth kNN distance calibration using 1 thread
+#> 21:51:43 Writing NN index file to temp file /tmp/Rtmp3dXLDZ/file1cba64d4d113
+#> 21:51:43 Searching Annoy index using 1 thread, search_k = 3000
+#> 21:51:43 Annoy recall = 100%
+#> 21:51:43 Commencing smooth kNN distance calibration using 1 thread
 #>  with target n_neighbors = 30
-#> 21:46:54 Initializing from normalized Laplacian + noise (using RSpectra)
-#> 21:46:54 Commencing optimization for 500 epochs, with 6160 positive edges
-#> 21:46:54 Using rng type: pcg
-#> 21:46:55 Optimization finished
+#> 21:51:44 Initializing from normalized Laplacian + noise (using RSpectra)
+#> 21:51:44 Commencing optimization for 500 epochs, with 6160 positive edges
+#> 21:51:44 Using rng type: pcg
+#> 21:51:45 Optimization finished
 
 as_AnnData(obj)
 #> Warning: Row names of `Loadings(seurat_obj, "pca")` do not match the expected var names