The R implementation of the Clustering-Informed Shared-Structure Variational Autoencoder (CISS-VAE). The Python implementation can be found here.
Installation
Install devtools or remotes if not already installed:
install.packages("remotes")
# or
install.packages("devtools")The rCISSVAE package can be installed with:
remotes::install_github("CISS-VAE/rCISS-VAE")
# or
devtools::install_github("CISS-VAE/rCISS-VAE")Ensuring correct virtual environment for reticulate
This package uses reticulate to interface with the python version of the package cissvae.
Therefore, it is necessary to make sure that you have a venv or conda environment set up that has the cissvae package installed.
If you are comfortable creating an environment and installing the package, great! Then all you need to do is tell reticulate where to point.
For Venv
reticulate::use_virtualenv("./.venv", required = TRUE)For conda
reticulate::use_condaenv("myenv", required = TRUE)Virtual environment helper function
If you do not want to manually create the virtual environment, you can use the helper function create_cissvae_env() to create a virtual environment (venv) in your current working directory.
create_cissvae_env(
envname = "cissvae_environment", ## name of environment
path = NULL, ## add path to wherever you want virtual environment to be
install_python = FALSE, ## set to TRUE if you want create_cisssvae_env to install python for you
python_version = "3.10" ## set to whatever version you want >=3.10. Python 3.10 or 3.11 recommended
)Once the environment is created, activate it using:
reticulate::use_virtualenv("./cissvae_environment", required = TRUE)
# In other words,
# reticulate::use_virtualenv("./your_environment_name", required = TRUE)