SoNNia modules in a Python script

In order to incorporate the core algorithm into an analysis pipeline (or to write your own script wrappers) all that is needed is to import the modules. Each module defines some classes that only a few methods get called on.

The modules are:

Module name	Classes
sonia.py	Sonia
sonnia.py	SoNNia
sonia_paired.py	SoniaPaired
sonnia_paired.py	SoNNiaPaired
classifiers.py	Linear, SoniaRatio
compare_repertoires.py	Compare
plotting.py	Plotter
utils.py	N/A (contains util functions)

The classes SoniaPaired, SoNNiaPaired, and SoNNia have similar behaviour to the ones defined in the SONIA <https://github.com/statbiophys/SONIA>_ package.

Basic Usage Examples

Linear single-chain model (equivalent to SONIA):

from sonnia.sonia import Sonia
qm = Sonia()

Deep non-linear single-chain model:

from sonnia.sonnia import SoNNia
qm = SoNNia()

Linear paired-chain model (e.g., alpha-beta for TCRs or heavy-light for BCRs):

from sonnia.sonia_paired import SoniaPaired
qm = SoniaPaired()

Deep non-linear paired-chain model:

from sonnia.sonnia_paired import SoNNiaPaired
qm = SoNNiaPaired()

Additional Utility Classes

Plotting and visualization:

from sonnia.plotting import Plotter
pl = Plotter(sonia_model)
pl.plot_model_learning("learning_curve.png")
pl.plot_vjl("marginals.png")

Repertoire comparison:

from sonnia.compare_repertoires import Compare
comparator = Compare(pgen_model="humanTRB", data=["data1.csv", "data2.csv"])
comparator.infer_models()
comparator.compute_distances()