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

if (FALSE) {

  # this command will install r-miniconda
  # and a giotto environment with all necessary python modules
  installGiottoEnvironment()
}