installGiottoEnvironment#
Last Updated: Mar 11, 2023
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#
|
all python modules (packages) that should be installed for Giotto to work |
|
python version to use within the giotto conda environment |
|
force reinstallation of miniconda |
|
force reinstallation of the giotto environment |
|
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)