Getting started

This section explains how to install and use the yomix tool.

Install via pip

In a Python virtual environment, do the following:

pip install yomix

Try the tool with the example dataset:

yomix --example

Install from Source

git clone https://github.com/perrin-isir/yomix.git

We recommend using micromamba to create a Python environment, but you can use any Python package manager instead.

cd yomix

micromamba create --name yomixenv --file environment.yaml

micromamba activate yomixenv

pip install -e .

Then try the tool with:

yomix yomix/example/pbmc.h5ad

To use it on your own files:

yomix yourfile.h5ad

where yourfile.h5ad is an AnnData object saved in .h5ad format (see anndata - Annotated data) with at least one .obsm field of dimension 2 or more.

Launch YOMIX from a jupyter notebook

Run those commands in a cell of your notebook:

import anndata
from yomix.server import start_server

xd = anndata.read_h5ad("yomix/example/pbmc.h5ad")
start_server(xd)

Improve reactiveness with subsampling

When there are many samples in the dataset, you can use the –subsampling option to improve reactiveness. This option will randomly subsample the dataset to a maximum number of N samples. For example:

yomix --subsampling 5000 yourfile.h5ad

This will subsample the dataset to a maximum of 5000 samples.