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Source: vignettes/lineaGT.Rmd
lineaGT.Rmd

Installing the package

The lineaGT R package can be installed directly from GitHub using devtools:

devtools::install_github("caravagnalab/lineaGT")

Once installed, load the package in your R session:

Installing Python dependencies

The lineaGT package relies on the Python module pylineaGT. The recommended approach is to install these Python dependencies inside a dedicated conda environment.

This can be done from R using the reticulate package through the following steps.

  • if Miniconda is not already available on your system, you can install it using through reticulate:
install_miniconda(path=miniconda_path(), update=TRUE, force=FALSE)
  • create a new conda environment with Python version 3.10:
reticulate::conda_create(envname="lineaGT", python_version="3.8")
  • activate the new conda environment within the current R session:
reticulate::use_condaenv("lineaGT")
  • install the pylineaGT Python module using pip inside the conda environment:
reticulate::conda_install(envname="lineaGT", packages="pylineaGT", pip=TRUE)

Fitting a lineaGT object

Before fitting a lineaGT object with the fit() or the fit_growth_rates() functions, make sure that the correct conda environment is active so that the pylineaGT module can be accessed:

reticulate::use_condaenv("lineaGT")

Functions that rely on pylineaGT include an additional argument, py, which allows you to explicitly pass the imported Python module. This ensures that the correct version of pylineaGT is used.

reticulate::use_condaenv("lineaGT")
py = reticulate::import("pylineaGT")
x = fit(..., py=py)
# or
x = fit_growth_rates(..., py=py)