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.
Usage
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.