Expose perplexity

r-seurat-scripts-post-install-tests.bats

@@ -179,6 +179,21 @@
     [ -f  "$tsne_seurat_object" ]
 }
 
+# Run t-SNE with perplexity
+
+@test "Run-tSNE analysis" {
+    if [ "$use_existing_outputs" = 'true' ] && [ -f "$tsne_seurat_object" ]; then
+        skip "$tsne_seurat_object exists and use_existing_outputs is set to 'true'"
+    fi
+
+    run rm -f $tsne_seurat_object && seurat-run-tsne.R -i $pca_seurat_object -r $reduction_type -d $dims_use -e NULL -o $tsne_seurat_object -b $tsne_embeddings_file --perplexity 20
+    echo "status = ${status}"
+    echo "output = ${output}"
+
+    [ "$status" -eq 0 ]
+    [ -f  "$tsne_seurat_object" ]
+}
+
 # Run marker detection
 
 @test "Find markers for each cluster" {

seurat-run-tsne.R

@@ -46,6 +46,13 @@ option_list = list(
     type = 'character',
     help = 'Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE'
   ),
+  make_option(
+    c("--perplexity"),
+    action = "store",
+    default = NULL,
+    type = 'integer',
+    help = 'Perplexity value for tSNE, if none is set, the default from seurat is used.'
+  ),
   make_option(
     c("-c", "--cells-use"),
     action = "store",
@@ -176,7 +183,8 @@ tsne_seurat_object <- RunTSNE( seurat_object,
                                cells = cells_use, 
                                dims = dims_use, 
                                seed.use = opt$random_seed, 
-                               add.iter = opt$add_iter, 
+                               add.iter = opt$add_iter,
+                               perplexity = opt$perplexity,
                                reduction.key = opt$reduction_key, 
                                reduction.name = opt$reduction_name, 
                                features = genes_use