Download a project's data files from the ScPCA Portal

Usage

download_project(
  project_id,
  destination = "scpca_data",
  format = "sce",
  merged = FALSE,
  include_multiplexed = NULL,
  overwrite = FALSE,
  redownload = FALSE,
  quiet = FALSE,
  unzip = TRUE,
  auth_token = Sys.getenv("SCPCA_AUTH_TOKEN")
)

Arguments

project_id: The ScPCA project ID (e.g. "SCPCP000001")
destination: The path to the directory where the unzipped file directory should be saved. Default is "scpca_data".
format: The desired file format, either "sce" (SingleCellExperiment), "anndata" (AnnData/H5AD), or "spatial" (for spatial data in Space Ranger format). Default is "sce".
merged: Download merged data files, if available. Default is FALSE.
include_multiplexed: Include multiplexed samples, if available. Default is TRUE for SingleCellExperiment and FALSE for AnnData and spatial samples, where multiplexed data are not available.
overwrite: Whether to overwrite files in existing directories if they already exist. Note that files in existing directories that do not have the same name as one of the downloaded files will not be deleted. Default is FALSE.
redownload: Whether to re-download if files from the same project and format already exist. If FALSE, existing files will be returned. Default is FALSE.
quiet: Whether to suppress download progress messages. Default is FALSE.
unzip: Whether to unzip the downloaded file. Default is TRUE. When FALSE, the zip file is saved directly to destination and its path is returned.
auth_token: An authorization token from get_auth(). Defaults to the SCPCA_AUTH_TOKEN environment variable, which get_auth() sets automatically.

Value

a vector of file paths for the downloaded files (invisibly)

Examples

if (FALSE) { # \dontrun{
# get_auth() stores the token in SCPCA_AUTH_TOKEN, so downloads pick it up automatically
get_auth("your.email@example.com", agree = TRUE)
# Then ask for a project download
download_project("SCPCP000001", destination = "scpca_data", format = "sce")

# Downloading merged files in AnnData format
download_project(
  "SCPCP000001",
  destination = "scpca_data",
  format = "anndata",
  merged = TRUE
)
} # }