README.md

In elagralinska/APLpackage: Association Plots

APL

When working with APL package please cite:

Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots
Elzbieta Gralinska, Martin Vingron
bioRxiv 2020.10.23.352096; doi: https://doi.org/10.1101/2020.10.23.352096

Installation

library(devtools)
install_github(" elagralinska/APL-Rpackage")

Pytorch installation

In order to speed up the singular value decomposition, we highly recommend the installation of pytorch. Users can instead also opt to use the slower R native SVD. For this, please turn the argument python = FALSE wherever applicable in this vignette.

Install pytorch with reticulate

library(reticulate)
install_miniconda() 
conda_install(envname = "r-reticulate", packages = "numpy")
conda_install(envname = "r-reticulate", packages = "pytorch")

Manually install pytorch with conda

Download the appropriate Miniconda installer for your system from the conda website. Follow the installation instructions on their website and make sure the R package reticulate is also installed before proceeding. Once installed, list all available conda environments via conda info --envs One of the environments should have r-reticulate in its name. Depending on where you installed it and your system, the exact path might be different. Activate the environment and install pytorch into it.

conda activate ~/.local/share/r-miniconda/envs/r-reticulate # change path accordingly.
conda install numpy
conda install pytorch

Feature overview

Please run

vignette("APL")

after installation for an introduction into the package.

elagralinska/APLpackage documentation built on Dec. 20, 2021, 4:15 a.m.