luctools: Analysis of Circadian Luciferase Time Series

luctools provides a toolset for plotting, detrending and calculating period and phase of luciferase based circadian expression experiments.

Motivation

To improve the ease of use and reproducibility of analysing circadian luciferase time series.

Features

Plotting of time series with mean and CIs calculated across replicates.
Detrending of signal for both decay and baseline.
Calculation and plotting of period and phase.

Example Usage

from luctools import analyse

#reads in data and sampling rate of experiment (samples/hour)
data = analyse.luctraces(path_to_input_data,sample_rate)
#plots undetrended data
data.gen_tsplot(output_path)

#detrends data
data.detrend()
#plots detrended data
data.gen_tsplot(output_path)

#calculates periods of each time series
data.get_periods()
#calculates phases of each time series
data.get_phases()
#plots period vs phase for each time series
data.gen_phase_plot(output_path)

A Note on Data Formatting

luctools expects input files to be formatted as comma seperated. The first column should index the observations. The header should start with any string and the rest of the header should contain the genotype of the observations in the column. Replicates should have the same column headers.

Frame	Control	Control	Control	Experimental	Experimental	Experimental
index#	data	data	data	data	data	data

Installation

pip install luctools

TO DO

Implement statistical comparison of phases between groups.
Improve phase determination.
Add API reference on readthedocs.

Built With

numpy
pandas
scipy
matplotlib
seaborn
peakutils

aleccrowell/luctools