Installs Python packages into a virtual environment

Install all Python packages used in the singleCellTK package using virtualenv_install from package reticulate. This will create a new virtual environment with the name envname if not already present.

sctkPythonInstallVirtualEnv(
  envname = "sctk-reticulate",
  packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama",
    "bbknn", "anndata"),
  selectEnvironment = TRUE,
  python = NULL
)

Arguments

envname

Character. Name of the virtual environment to create.

packages

Character Vector. List of packages to install.

selectEnvironment

Boolean. Run selectSCTKVirtualEnvironment after installing all packages to select the virtual environment. Default TRUE.

python

The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

Value

None. Installation of virtual environment.

See also

See virtualenv_create for more information on creating a Conda environment. See virtualenv_install for more description of the installation parameters. See https://rstudio.github.io/reticulate/ for more information on package reticulate. See selectSCTKVirtualEnvironment for reloading the virtual environment if R is restarted without going through the whole installation process again.

Examples

if (FALSE) {
sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
}