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