Project full data to the sketch assay — ProjectData • Seurat

This function allows projection of high-dimensional single-cell RNA expression data from a full dataset onto the lower-dimensional embedding of the sketch of the dataset.

ProjectData(
  object,
  assay = "RNA",
  sketched.assay = "sketch",
  sketched.reduction,
  full.reduction,
  dims,
  normalization.method = c("LogNormalize", "SCT"),
  refdata = NULL,
  k.weight = 50,
  umap.model = NULL,
  recompute.neighbors = FALSE,
  recompute.weights = FALSE,
  verbose = TRUE
)

Arguments

object: A Seurat object.
assay: Assay name for the full data. Default is 'RNA'.
sketched.assay: Sketched assay name to project onto. Default is 'sketch'.
sketched.reduction: Dimensional reduction results of the sketched assay to project onto.
full.reduction: Dimensional reduction name for the projected full dataset.
dims: Dimensions to include in the projection.
normalization.method: Normalization method to use. Can be 'LogNormalize' or 'SCT'. Default is 'LogNormalize'.
refdata: An optional list for label transfer from sketch to full data. Default is NULL. Similar to refdata in `MapQuery`
k.weight: Number of neighbors to consider when weighting labels for transfer. Default is 50.
umap.model: An optional pre-computed UMAP model. Default is NULL.
recompute.neighbors: Whether to recompute the neighbors for label transfer. Default is FALSE.
recompute.weights: Whether to recompute the weights for label transfer. Default is FALSE.
verbose: Print progress and diagnostic messages.

Value

A Seurat object with the full data projected onto the sketched dimensional reduction results. The projected data are stored in the specified full reduction.