To reproduce the figures shown in the manuscript run the following scripts.
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
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
fig1-macosko.py
fig3-iris.py
fig5-tasic.py
fig6-cao.py
fig7-hocherner.py