Skip to contents

Map a SingleCells query onto a Symphony reference

map_symphony_query.Rd

Projects query cells through the reference's PCA loadings and applies the cached MoE batch correction. Gene matching is by name against the reference's stored HVG names; unmatched HVGs become zero columns. Results are attached to the query as embeddings.

Usage

map_symphony_query(
  reference,
  query,
  batch_column = NULL,
  additional_batch_columns = NULL,
  params = params_symphony_map(),
  .verbose = TRUE
)

Arguments

reference

SymphonyReference.

query

SingleCells query.

batch_column

Optional string. If NULL, no batch correction is applied (z_corr = z_pca).

additional_batch_columns

Optional character vector.

params

List. Output of params_symphony_map().

.verbose

Boolean or integer.

Value

The query object with embeddings "symphony" (z_corr), "symphony_pca" (z_pca) and "symphony_r" (soft cluster assignments, transposed to N_q x K).

Examples

# project a second data set into the reference embedding
ref <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 500L,
    n_genes = 50L,
    n_batches = 2L
  )
)
symphony_ref <- build_symphony_ref(
  ref,
  batch_column = "batch_index",
  hvg = get_hvg(ref) + 1L,
  harmony_params = params_sc_harmony(k = 10L),
  no_pcs = 10L,
  .verbose = FALSE
)
query <- demo_single_cells(prepped = FALSE, seed = 7L)
query <- map_symphony_query(symphony_ref, query = query, .verbose = FALSE)
dim(get_embedding(query, "symphony"))
#> [1] 500  10

unlink(c(ref@dir_data, query@dir_data), recursive = TRUE, force = TRUE)