scExploreR config app — run_config • scExploreR

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
)

object_path: path to a single-cell object to be configured. Currently, Seurat, SingleCellExperiment, and anndata objects are supported. For SingleCellExperiment objects with using HDF5 disk-backed storage via HDF5Array, object_path should be a path to the directory containing the se.rds and assays.h5 files for the 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 HDF5Array::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.