Extract embedding coordinates for plotting — extract_embedding

Pulls an embedding into a long data.table with standardised coordinate columns (dim_1, dim_2, ...) and, optionally, observation metadata. The embedding name is stored as an embedding attribute for axis labelling.

Usage

extract_embedding_data(object, embedding, obs_cols = NULL, ...)

Arguments

object: A single cell class.
embedding: String. Name of the embedding (e.g. "umap", "pca").
obs_cols: Optional character vector. Obs columns to attach.
...: Additional arguments forwarded to get_embedding() (e.g. modality).

Value

A data.table with cell_id, dim_* columns and any requested obs columns.

Examples

# PCA coordinates with a cell annotation riding along
sc <- demo_single_cells()
dt <- extract_embedding_data(sc, "pca", obs_cols = "cell_grp")
head(dt[, c("cell_id", "dim_1", "dim_2", "cell_grp")])
#>     cell_id     dim_1      dim_2    cell_grp
#>      <char>     <num>      <num>      <char>
#> 1: cell_001 -0.369421  3.0682011 cell_type_1
#> 2: cell_002  2.233128 -2.5044506 cell_type_2
#> 3: cell_003 -2.483406  0.5060491 cell_type_3
#> 4: cell_004  1.357756  2.6232290 cell_type_1
#> 5: cell_005  2.134258 -0.2906672 cell_type_2
#> 6: cell_006 -2.623219  0.5387377 cell_type_3

unlink(sc@dir_data, recursive = TRUE, force = TRUE)