getSpatialDataset#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/general_help.R#L635

Description#

This package 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", "Human_PCa_scRNAseq", "Mouse_brain_scRNAseq"),
  directory = getwd(),
  ...
)

Arguments#

Argument

Description

dataset

dataset to download

directory

directory to save the data to

list()

additional parameters to download file