Generate a UMAP for a sketched assay and then project it to the full data.

This is a wrapper function that builds on the ProjectUMAP() function, which allows users to generate UMAP for a subset of the data (e.g., cells from a sketched assay), and then project this UMAP to any other data.

Usage

RunAndProjectUMAP(
  object,
  nn.name = NULL,
  k.nn = 5,
  landmark.assay.name = "LANDMARK",
  reduction.name = "sketched.umap",
  verbose = TRUE,
  ...
)

Arguments

object: a Seurat object
nn.name: the name of the Neighbor object used to generate the UMAP.
k.nn: the number of neighbors used to genearte the UMAP. If it exceeds the number of k in the nn.name object, will be ignored.
landmark.assay.name: the name of the sketched assay
reduction.name: the name of the UMAP to be stored; Note that the projected UMAP will be named as "proj.'reduction.name'".
verbose: Print progress status
...: other parameters that are accepted by RunUMAP() or ProjectUMAP()

Value

return a Seurat object that contains a UMAP of the sketched assay and a UMAP of the full data