installGiottoEnvironment: installGiottoEnvironment

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

installGiottoEnvironment

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",
  mini_install_path = NULL,
  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
mini_install_path	(optional) desired location miniconda installation. If not provided, it is chosen by reticulate::install_miniconda() Note the required input format: Correct format –> mini_install_path = "C:/my/conda/lives/here" OR "C:\my\conda\lives\here" INCORRECT formats –> mini_install_path = "C:/my/conda/lives/here/" AND "C:\my\conda\lives\here\"
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)

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.