ProjectData {Seurat}

Project full data to the sketch assay

Description

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.

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.