Project query data to the reference dimensional reduction

Project query data to the reference dimensional reduction

ProjectCellEmbeddings(query, ...)

# S3 method for class 'Seurat'
ProjectCellEmbeddings(
  query,
  reference,
  query.assay = NULL,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  normalization.method = c("LogNormalize", "SCT"),
  scale = TRUE,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

# S3 method for class 'Assay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

# S3 method for class 'SCTAssay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

# S3 method for class 'StdAssay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

# Default S3 method
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  features = NULL,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

# S3 method for class 'IterableMatrix'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  features = features,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  block.size = 10000,
  ...
)

Arguments

query

An object for query cells

reference

An object for reference cells

query.assay

Assay name for query object

reference.assay

Assay name for reference object

reduction

Name of dimensional reduction from reference object

dims

Dimensions used for reference dimensional reduction

scale

Determine if scale query data based on reference data variance

verbose

Print progress

feature.mean

Mean of features in reference

feature.sd

Standard variance of features in reference

Value

A matrix with projected cell embeddings