Co-embed reference and query cells

Impute reference expression into query cells with TransferData, merge reference and query cells, and compute PCA/UMAP on the shared expression space. The current implementation mirrors the Seurat ATAC integration vignette for ATAC query and RNA reference.

Usage

RunCoEmbedding(
  srt,
  reference,
  assay = NULL,
  reference_assay = NULL,
  reference_reduction = "pca",
  reference_dims = 1:30,
  gene_activity_assay = "ACTIVITY",
  weight_reduction = NULL,
  dims = 2:30,
  genes_use = NULL,
  imputed_assay = "RNA",
  modality_col = "modality",
  coembed_prefix = "CoEmbed",
  npcs = 30,
  umap_dims = 1:30,
  k.weight = 100,
  verbose = TRUE,
  seed = 11
)

Arguments

srt

A Seurat object.

reference

RNA reference Seurat object used for label transfer.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

reference_assay

Assay used in the reference object.

reference_reduction

Reduction used in the reference object.

reference_dims

Dimensions used from the reference reduction.

gene_activity_assay

Name of the gene activity assay used for mapping.

weight_reduction

Reduction in srt used to weight transferred labels. If NULL, an ATAC linear reduction is resolved automatically from ATAC_default_linear_reduction, {prefix}lsi, {prefix}svd, or the current default reduction.

dims

Query reduction dimensions used by TransferData.

genes_use

Genes/features used for expression imputation and co-embedding. If NULL, reference variable features are used.

imputed_assay

Assay name for imputed RNA expression in ATAC cells.

modality_col

Metadata column storing RNA/ATAC origin after merge.

coembed_prefix

Prefix for co-embedding reductions.

npcs

Number of PCs to compute.

umap_dims

PC dimensions used for UMAP.

k.weight

Number of neighbors used when weighting transfer anchors.

verbose

Whether to print the message. Default is TRUE.

seed

Random seed used for UMAP.

Value

A merged Seurat object containing RNA reference and ATAC query cells.