cytomulate

A simulation package for Cytometry by Time-of-Flight (CyTOF)

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Installation

You can easily install cytomulate from either PyPI or conda. For the former, use the following command:

pip install cytomulate

Or if you are using a conda environment, you can use the following command:

conda install -c normalizingflow cytomulate

If you wish to use PyCytoData, you can install separately with more instructions here.

Dependencies

Good news: we didn't have to write cytomulate from scratch in assembly language! This means that we will need dependencies to install it. Below is a list of packages that you will need:

• numpy
• scipy
• scikit-learn
• networkx
• matplotlib
• tqdm

Most of these are pretty standard! And even better news: the installation instructions should automatically handle all the dependency issues. If you have a problem with installation, let us know and we're happy to help!

While the above are all core dependencies, we highly highly highly highly highly recommend PyCytoData as well! You can get all the benefits of an integrated pipeline! But of course, for those of you who don't fancy more dependencies, we understand as well!

Examples

We have two modes: Creation Mode and Emulation Mode. The former is probabilistic-model based simulation without the need of datasets; the latter is based on existing datasets to match as much of the existing features as possible. Here, we give two quick examples of how they work.

Creation Mode

To create your datasets, you can run the following:

>>> from cytomulate import CreationCytofData
>>> cytof_data = CreationCytofData()
>>> cytof_data.initialize_cell_types()
>>> expression_matrices, labels, _, _ = cytof_data.sample(n_samples = 1000)

The expression_matrices is a dictionary that contains the expression matrix from each sample. Correspondingly, labels is a dictionary that contains their cell types.

Emulation Mode

This is a little bit more involved because we need existing data! If you already have your data, congratulations, you are good to go! For this demonstration, we use PyCytoData to load some example datasets instead (Of course, you will need to install PyCytoData first if you wish to use it):

>>> from cytomulate import EmulationCytoData
>>> from PyCytoData import DataLoader

>>> exprs = DataLoader.load_dataset(dataset="levine13")
>>> exprs.preprocess(arcsinh=True)
>>> cytof_data = EmulationCytofData()
>>> cytof_data.initialize_cell_types(expression_matrix=exprs.expression_matrix,
...                                  labels=exprs.cell_types)
>>> expression_matrices, labels, _, _ = cytof_data.sample(n_samples = 1000)

This is it!

Working with PyCytoData

We're fully compatible with PyCytoData! As you've seen above, you can use PyCytoData to download datasets! If you're familiar with that interface and in love with its easy workflow, you can have cytomulate output a PyCytoData object as well:

>>> from cytomulate import CreationCytofData
>>> cytof_data = CreationCytofData()
>>> cytof_data.initialize_cell_types()
>>> simulation_data = cytof_data.sample_to_pycytodata(n_samples = 1000)

This will allow you to use all the downstream capabilities of PyCytoData.

Command-Line Interface (CLI)

If you prefer to use cytomulate from the command-line, you've got that option as well! One caveat is that this mode requires PyCytoData to be installed. To run the Creation Mode, you can do:

python -m cytomulate \
	--creation \
	--n_cells 1000 \
	-o <your_dir_here>

To run the emulation mode, you can run the following:

python -m cytomulate \
	--emulation \
	--n_cells 1000 \
	-o <your_dir_here> \
	--exprs <you_path_to_exprssion_matrix> \
	--cell_types <you_path_to_cell_types>

Of course, we have much more customization options! For more details, read our tutorial here.

Documentation

For more detailed documentation on cytomulate, please visit our website! You will find detailed tutorials, guidelines, development guides, etc.

Our documentation is built automatically on the cloud! If you wish to build locally, check our detailed guide here!

Latest Release: v0.2.0

Welcome to Cytomulate v0.2.0! Hooray! We are not only bringing documentation enhancements, but we are also introducing a new feature for more accurate simulations!

Changes and New Features

• The utilities.univariate_noise_model() method:
  • Added half_normal option to the noise_distribution parameter
  • Changed the default noise_distribution to uniform (This is a breaking change because of the benefits to simulated results).
  • A warning is given when no user-specified noise_distribution is supplied to warn the breaking change
• Added the utilities.estimate_noise_model() method to estimate the noise present in the data
• Added a built-in estimation procedure to match the amount of zeroes observed in the dataset

Improvements

• Added 4 more detailed tutorials on our documentation website <https://cytomulate.readthedocs.io>_
• Improved docstrings with more details on key parameters
• Updated the lastest references and links

References

If you are cytomulating in your workflow, citing our paper is appreciated:

@article {Yang2022.06.14.496200,
	author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
	title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data},
	elocation-id = {2022.06.14.496200},
	year = {2022},
	doi = {10.1101/2022.06.14.496200},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200},
	eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf},
	journal = {bioRxiv}
}