Get UMAP data and plot from Seurat object. — getUMAP • scMiko

Get UMAP data and plot from Seurat object.

getUMAP(
  object,
  umap.key = "umap",
  node.type = "point",
  meta.features = colnames(object@meta.data),
  size = autoPointSize(ncol(object)),
  ...
)

Arguments

object: Seurat Object.
umap.key: Character UMAP key slot in seurat object. Default is "umap"
node.type: "point" or "text"
meta.features: character vector specifying which meta features to retrieve. Default is `colnames(object@meta.data)`
...: additional parameters to geom_point or geom_text

Value

list containing UMAP data.frame and ggplot handle

Author

Nicholas Mikolajewicz

Examples


wnnUMAP.list <- getUMAP(so.gene, umap.key = "wnn.umap", node.type = "text")
#> Error in data.frame(object@reductions[[umap.key]]@cell.embeddings): object 'so.gene' not found

df.wnn.umap <- wnnUMAP.list$df.umap
#> Error in eval(expr, envir, enclos): object 'wnnUMAP.list' not found
plt.wnn.umap <- wnnUMAP.list$plt.umap
#> Error in eval(expr, envir, enclos): object 'wnnUMAP.list' not found