maldi_PIKE — Peak Information KErnel for MALDI-TOF MS spectra
maldi_PIKE is a small library for Python 3 that include the code used for
'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass
spectra'. The main method includes PIKE, the Peak Information KErnel for MALDI-TOF MS spectra,
embedded in a Gaussian Process. We developed PIKE based on heat diffusion on structured
objects. It is well suited for MALDI-TOF mass spectra and able to capture interactions between
mass peaks.
Dependencies
- Python 3.7
- packages listed in
pyproject.toml
Installation
- Clone the repository
poetry install
Follow the instructions given by poetry.
Example behaviour of PIKE
Figure 2:
Code to recreate this graphic in matplotlib can be found in
ismb2020_maldi/visualise_feature_map.py. Use the script as
follows:
poetry run python ismb2020_maldi/visualise_feature_map.py data/Example_peaks.txt
This should result in the following plot:
This repository is work in progress.