Skip to contents

Generate source-pure meta cells and merge them

meta_cells_per_group.Rd

Splits object by group_col, optionally runs pipeline on each subset, generates meta cells per group and merges the results into a single MetaCells() object. This gives you meta cells that never mix cells from two patients/samples, while still being one object you can run SCENIC, AUCell or NMF over.

The meta cell generators need an embedding, so pipeline will normally be step_hvg_sc() %>>% step_pca_sc() %>>% step_neighbours_sc() unless every subset already carries one.

Usage

meta_cells_per_group(
  object,
  group_col,
  method = c("bootstrapped", "seacells", "supercells"),
  mc_params = list(),
  pipeline = NULL,
  groups = NULL,
  feature_space = c("intersect", "union"),
  .verbose = TRUE
)

Arguments

object

SingleCells.

group_col

String. Column in obs used to split.

method

String. One of c("bootstrapped", "seacells", "supercells"). Picks the meta cell generator.

mc_params

Named list. Arguments passed on to the generator, e.g. list(sc_meta_cell_params = params_sc_bt_metacells(), target_size = 1e5).

pipeline

Optional ScPipeline applied to each subset before the meta cells are generated.

groups

Optional character vector. Restrict to these group values; if NULL, all unique values of group_col are used.

feature_space

String. One of c("intersect", "union"). Passed to merge_meta_cells(). Irrelevant here as all groups share the gene space of the parent object.

.verbose

Boolean. Controls verbosity of the function.

Value

A merged MetaCells() object with a source_id column in its observation table.

Examples

# meta cells that never mix two cell groups
sc <- demo_single_cells(prepped = FALSE)
prep <- step_hvg_sc(hvg_no = 30L, .verbose = FALSE) %>>%
  step_pca_sc(no_pcs = 10L, .verbose = FALSE) %>>%
  step_neighbours_sc(.verbose = FALSE)
meta_cells_per_group(
  object = sc,
  group_col = "cell_grp",
  method = "bootstrapped",
  mc_params = list(
    sc_meta_cell_params = params_sc_bt_metacells(target_no_metacells = 10L),
    .verbose = FALSE
  ),
  pipeline = prep,
  .verbose = FALSE
)
#> Single cell experiment (Meta Cells).
#>   Meta cell method: meta_cells_hdwgcna
#>   Merged: TRUE
#>   No meta cells: 30
#>   No genes: 50
#>   No cells aggregated: 297
#>   No obs rows in source: 500
#>   HVG calculated: FALSE
#>   PCA calculated: FALSE
#>   Other embeddings: none
#>   KNN generated: FALSE
#>   SNN generated: FALSE
#>   Stale artefacts: none

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