installGiottoEnvironment: installGiottoEnvironment

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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 and provide the instructions to the createGiottoObject function.

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()

  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


## End(Not run)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.