run_config() will launch a Shiny app used to configure datasets for use in the main browser.
Usage
run_config(
object_path,
config_path = NULL,
is_HDF5SummarizedExperiment = FALSE,
HDF5_prefix = "",
dev_mode = FALSE
)Arguments
- object_path
relative or absolute path to the Seurat object to be configured. The file provided must be a .rds file created from a single Seurat object.
- config_path
optional: if provided, the data from this file will be loaded when the user selects "load config file" in the config app. This should be a YAML file, though .rds files from versions 0.4.0 and earlier will also be accepted.
- is_HDF5SummarizedExperiment
Set this to TRUE to load an HDF5-enabled SingleCellExperiment object saved via saveHDF5SummarizedExperiment. When loading an HDF5-enabled object, set the object_path to the directory of the HDF5-enabled object, created when saving the object via HDF5Array:saveHDF5SummarizedExperiment.
- HDF5_prefix
When loading an HDF5-backed SingleCellExperiment HDF5_prefix is passed to the prefix parameter of HDF5Array::loadHDF5SummarizedExperiment to specify the prefixes for the se.rds and assays.h5 files.
- dev_mode
Used only for development. If TRUE, the server values for each option chosen by the user will be printed at the bottom of the "general" tab.