Run monocle3 on Seurat object
Usage
RunMonocle3(
SeuratObj,
batch = NULL,
reduction_method = "UMAP",
keep_orig_reduction = TRUE,
root_clusters = NULL,
save_plot = TRUE,
return_object = TRUE
)Arguments
- SeuratObj
A Seurat object
- batch
one column of
SeuratObj@meta.data, indicating batch effect.- reduction_method
reduction method, UMAP as default.
- keep_orig_reduction
keep original reduction dimension of Seurat object.
- root_clusters
seurat clusters used to help identify the root.
- save_plot
save plots to pdf or not.
- return_object
return CellDataSet object or not.