Download example datasets for CoPro vignettes

Downloads pre-processed, subsampled datasets from GitHub Releases for use in vignettes and tutorials. The datasets are attached to GitHub releases via the piggyback package.

Usage

copro_download_data(
  dataset = c("colon_d3", "colon_d9", "kidney", "organoid", "brain_merfish"),
  destdir = NULL,
  tag = "data-v1",
  overwrite = FALSE
)

Arguments

dataset

Character string specifying which dataset to download. One of "colon_d3", "colon_d9", "kidney", "organoid", or "brain_merfish".

destdir

Directory to save the downloaded file. Defaults to a package-specific cache directory via tools::R_user_dir().

tag

The GitHub release tag to download from. Defaults to "data-v1".

overwrite

Logical; if TRUE, re-download even if the file already exists locally. Default FALSE.

Value

The file path to the downloaded RDS file (invisibly).

Details

Available datasets:

colon_d3

Colon Day 3 organoid data (Epithelial, Fibroblast, Immune). Demonstrates cross-cell-type co-progression with orthogonal CCA axes.

colon_d9

Colon Day 9 organoid data (multiple slides). Demonstrates multi-slide analysis and score transfer.

kidney

Kidney seqFISH data (tubular and vascular cells). Demonstrates supervised/guided spatial gradient detection.

organoid

72hr organoid culture (single cell type). Demonstrates within-cell-type spatial pattern detection.

brain_merfish

Brain MERFISH data (D1/D2 neurons). Demonstrates two-cell-type co-progression.

The data files are hosted as GitHub Release assets and are typically 5–30 MB each. They are subsampled from the full datasets to allow fast vignette execution while preserving biological signal.

Examples

if (FALSE) { # \dontrun{
# Download and load the colon D3 dataset
path <- copro_download_data("colon_d3")
dat <- readRDS(path)
} # }