To reproduce the experiments reported in the paper, do the following:
- Install the Mapper package
- Install the dependencies
- R packages needed: data.table, ks, fastICA, RANN, reticulate, parallelDist
- Python package needed: numpy, scikit-learn, umap-learn
- Open the notebook
multiscale_benchmarks.Rmdin Rstudio and click 'Run all'
- The figures require ggplot2 and gridExtra to be installed
I use reticulate+miniconda to manage and load the python dependencies, and the path needs to be set to an appropriate conda environment with the above dependencies to run.