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msalign: Signal calibration and alignment by reference peaks

Project description

msalign - signal calibration and alignment

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This package was inspired by MATLAB's msalign function which allows alignment of multiple signals to reference peaks.

Installation

Install from PyPi

pip install msalign

Install directly from GitHub

pip install -e git+https://github.com/lukasz-migas/msalign.git

Install in development mode

python setup.py develop

Usage

Usage is relatively straightforward. Simply import msalign from the package and provide x, array and peaks values. msalign accepts a lot of other parameters that might improve your alignment - simply provide them as keyword parameters.

import numpy as np
from msalign import msalign


filename = r"./example_data/msalign_test_data.csv"
data = np.genfromtxt(filename, delimiter=",")
x = data[1:, 0]
array = data[1:, 1:].T
peaks = [3991.4, 4598, 7964, 9160]

aligned = msalign(x, array, peaks, weights=[60, 100, 60, 100], only_shift=False)

png

Zoom-in on each peak the spectrum was aligned against

png

Reference

Monchamp, P., Andrade-Cetto, L., Zhang, J.Y., and Henson, R. (2007) Signal Processing Methods for Mass Spectrometry. In Systems Bioinformatics: An Engineering Case-Based Approach, G. Alterovitz and M.F. Ramoni, eds. Artech House Publishers).

MATLAB's msalign

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