Reduce n.neighbors for umap calc base on cell #

r.scripts/sc-TissueMapper_functions.R

@@ -602,7 +602,13 @@ scCluster <- function(sc10x,res=0.1,red="pca",dim,print="umap",folder=FALSE,assa
 
   #Calculste Vis
   #sc10x <- RunTSNE(sc10x,dims=1:dim,reduction="pca",assay=assay)
-  sc10x <- RunUMAP(sc10x,dims=1:dim,reduction="pca",assay=assay)
+  
+  if (ncol(sc10x) > 30) {
+    n.neighbors <- 30
+  } else if (ncol(sc10x.temp) <= 30) {
+    n.neighbors <- ncol(sc10x)-1
+  }
+  sc10x <- RunUMAP(sc10x,dims=1:dim,reduction="pca",assay=assay,n.neighbors=n.neighbors)
   
   sc10x <- FindNeighbors(sc10x,reduction=red,verbose=FALSE,assay=assay)