This function will automatically download the spatial locations and expression matrix for the chosen dataset. These files are already in the right format to create a Giotto object. If wget is installed on your machine, you can add 'method = wget' to the parameters to download files faster.
Usage
getSpatialDataset(
dataset = c("ST_OB1", "ST_OB2", "codex_spleen", "cycif_PDAC", "starmap_3D_cortex",
"osmfish_SS_cortex", "merfish_preoptic", "mini_seqFISH", "seqfish_SS_cortex",
"seqfish_OB", "slideseq_cerebellum", "ST_SCC", "scRNA_prostate", "scRNA_mouse_brain",
"mol_cart_lung_873_C1", "sg_mini_kidney"),
directory = getwd(),
verbose = TRUE,
dryrun = FALSE,
...
)Arguments
- dataset
dataset to download
- directory
directory to save the data to
- verbose
verbosity
- dryrun
dryrun: does not download data but shows download commands
- ...
additional parameters to
download.file