# Figures

To reproduce the figures shown in the manuscript run the following scripts.

## Download data

To download the raw data files and apply the same preprocessing techniques, run

    bash generate_h5ad.sh

This script generates `.h5ad` files, which are much easier (and faster) to work with. However, generating these fiels can take a very long time, so we have uploaded the already prepared `.h5ad` files to `file.biolab.si/opentsne`. To download the required files, run

    bash download_h5ad.sh

## Generate figures

Once you have obtained the preprocessed .h5ad files, you can replicate the exact conda environment used to generate the figures from the manuscript. The environment can be installed and activated by running

    conda env create -f conda-environment.yml
    conda activate tsne-paper

The figures (excluding benchmarks) from the manuscript can then be generated by running

    bash generate_figures.sh

## Scripts

### `fig1-macosko.py`

### `fig3-iris.py`

### `fig5-tasic.py`

### `fig6-cao.py`

### `fig7-hocherner.py`