Skip to contents

Append data from an h5Seurat file to a preexisting Seurat object

Source: R/AppendData.R
AppendData.Rd

Append data from an h5Seurat file to a preexisting Seurat object

Usage

AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for class 'character'
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for class 'H5File'
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for class 'h5Seurat'
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

file

Name of an h5Seurat file path (character) or connected h5Seurat file

object

A Seurat object to append data to

assays

One of:

  • A character vector with names of assays

  • A character vector with one or more of counts, data, scale.data describing which slots of all assays to load

  • A named list where each entry is either the name of an assay or a vector describing which slots (described above) to take from which assay

  • NULL for all assays

  • FALSE for no assays

reductions

One of:

  • NULL (default): Load all reductions (PCA, UMAP, etc.)

  • A character vector with names of specific reductions (e.g., c("pca", "umap"))

  • NA: Load only global (assay-independent) reductions

  • FALSE: Skip loading all reductions

Note: Only reductions associated with a loaded assay or marked as global will be loaded.

graphs

One of:

  • NULL (default): Load all graphs

  • A character vector with specific graph names (e.g., c("RNA_snn", "ADT_snn"))

  • FALSE: Skip loading graphs

Note: Only graphs associated with loaded assays will be available.

images

One of:

  • NULL (default): Load all images (for spatial experiments)

  • A character vector with image names

  • NA: Load only global images

  • FALSE: Skip images

extras

Extra information to load; supports any combination of the following values:

“commands”

Load command logs. If overwrite = TRUE, replaces existing command logs

overwrite

Overwrite existing data in object with data from file

verbose

Logical; if TRUE (default), show progress messages

...

Arguments passed to other methods

Value

object with the extra data requested