Hi R community,
I am trying to show a dimplot graph with a object reduced with umap. However, I cannot run this and it response me with "An exception occurred". I can demonstrate the graphs of VlnPlot and ElbowPlot in the response section but just not DimPlot. Can anyone tell me how to fix this problem? Thank you.
#* clustering_umap
#* serializer png
#* @post /clustering_umap
clustering_umap <- function(dims, resolution){
seurat_obj <- uploaded_file
dims <- as.numeric(dims)
resolution <- as.numeric(resolution)
seurat_obj <- FindNeighbors(seurat_obj, dims = 1:dims) #dims = dimensions
seurat_obj <- FindClusters(seurat_obj, resolution = resolution)
seurat_obj <- RunUMAP(seurat_obj, dims = 1:dims)
# SaveSeuratRds(seurat_obj, file='clustering_umap.RDS')
p <- DimPlot(seurat_obj, reduction = "umap")
print(p)
uploaded_file <<- seurat_obj
}