Project Query Data Onto PCA Space of Reference Data

This function projects a query singleCellExperiment object onto the PCA space of a reference singleCellExperiment object. The PCA analysis on the reference data is assumed to be pre-computed and stored within the object.

projectPCA(
  query_data,
  reference_data,
  query_cell_type_col,
  ref_cell_type_col,
  pc_subset = 1:10,
  assay_name = "logcounts"
)

Arguments

query_data

A SingleCellExperiment object containing numeric expression matrix for the query cells.

reference_data

A SingleCellExperiment object containing numeric expression matrix for the reference cells.

query_cell_type_col

character. The column name in the colData of query_data that identifies the cell types.

ref_cell_type_col

character. The column name in the colData of reference_data that identifies the cell types.

pc_subset

A numeric vector specifying the subset of principal components (PCs) to compare. Default is 1:10.

assay_name

Name of the assay on which to perform computations. Defaults to "logcounts".

Value

A data.frame containing the projected data in rows (reference and query data combined).

Details

This function assumes that the "PCA" element exists within the reducedDims of the reference data (obtained using reducedDim(reference_data)) and that the genes used for PCA are present in both the reference and query data. It performs centering and scaling of the query data based on the reference data before projection.

Author

Anthony Christidis, anthony-alexander_christidis@hms.harvard.edu

Examples

# Load data
data("reference_data")
data("query_data")

# Project the query data onto PCA space of reference
pca_output <- projectPCA(query_data = query_data,
                         reference_data = reference_data,
                         query_cell_type_col = "SingleR_annotation",
                         ref_cell_type_col = "expert_annotation",
                         pc_subset = 1:10)