installGiottoEnvironment#

Last Updated: Jan 14, 2025

Description#

Installs a giotto environment

Usage#

installGiottoEnvironment(
  packages_to_install = c("pandas==1.5.1", "networkx==2.8.8", "python-igraph==0.10.2",
    "leidenalg==0.9.0", "python-louvain==0.16", "python.app==1.4", "scikit-learn==1.1.3"),
  python_version = "3.10.2",
  force_miniconda = FALSE,
  force_environment = FALSE,
  verbose = TRUE
)

Arguments#

`packages_to_install`	all python modules (packages) that should be installed for Giotto to work
`python_version`	python version to use within the giotto conda environment
`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 and provide the instructions to the createGiottoObject function.

By default, Python v3.10.2 will be used with the following python modules for Giotto Suite implementations:

- pandas==1.5.1
- networkx==2.8.8
- python-igraph==0.10.2
- leidenalg==0.9.0
- python-louvain==0.16
- python.app==1.4
- scikit-learn==1.1.3

The giotto environment can be custom installed by changing the python_version parameter and module versions in the packages_to_install parameter.

For example, this giotto environment works as well, and was the default environment status for past releases of Giotto. Python v3.6

- pandas==1.1.5
- networkx==2.6.3
- python-igraph==0.9.6
- leidenalg==0.8.7
- python-louvain==0.15
- python.app==2 # macOS only
- scikit-learn==0.24.2

Value#

installs a giotto environment using the reticulate miniconda system

Examples#

## Not run:

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

## End(Not run)