installGiottoEnvironment#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/python_environment.R#L268

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"),
  python_version = "3.6",
  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

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.

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()

By default python v3.6 will be  used with the following python modules:
- 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

A more recent giotto environment can be installed by changing the python_version parameter
and module versions in the packages_to_install parameter:

For example this giotto environment is know to work:
python_version = '3.8.10'

and modules:
- pandas==1.3.1
- networkx==2.6.2
- python-igraph==0.9.6
- leidenalg==0.8.7
- python-louvain==0.15
- python.app==2 [mac OSX only]
- scikit-learn==1.0.2