Install Giotto Environment

installGiottoEnvironment()

Installs a Giotto environment

installGiottoEnvironment(
    packages_to_install = c("pandas", "networkx", "python-igraph", "leidenalg",
        "python-louvain", "python.app", "scikit-learn"),
    force_miniconda = FALSE,
    force_environment = FALSE,
    verbose = TRUE
)

Arguments

packages_to_install	all python modules (packages) that should be installed for Giotto to work
force_miniconda	force reinstallation of miniconda
force_environment	force reinstallation of the giotto environment
verbose	be verbose

Value

Installs a Giotto environment using the reticulate miniconda system

Details

This function will install a local giotto environment using the miniconda system as implemented by reticulate. Once this giotto environment is installed it will be automatically detected when you run the Giotto toolbox. If you want to use your own python path then you can set the python_path in the createGiottoInstructions and provide the instructions to the createGiottoObject function.

Examples

This command will install an r-miniconda and a Giotto environment with all of the necessary python modules.

if (FALSE) {installGiottoEnvironment()}