`installGiottoEnvironment`¶

installGiottoEnvironment

Description¶

Installs a giotto environment

Usage¶

installGiottoEnvironment(
  packages_to_install = c("pandas==1.1.5", "networkx==2.6.3", "python-igraph==0.9.6",
    "leidenalg==0.8.7", "python-louvain==0.15", "python.app==2", "scikit-learn==0.24.2"),
  force_miniconda = FALSE,
  force_environment = FALSE,
  verbose = TRUE
)

Arguments¶

Argument	Description
`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

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` <#creategiottoinstructions>`_ and provide the instructions to the ``createGiottoObject` <#creategiottoobject>`_ function.

Value¶

installs a giotto environment using the reticulate miniconda system

Examples¶

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

The following python modules will be installed:
- pandas==1.1.5
- networkx==2.6.3
- python-igraph==0.9.6
- leidenalg==0.8.7
- python-louvain==0.15
- python.app==2 [mac OSX only]
- scikit-learn==0.24.2