The analyze_plate_reader_growth from churchlab

analyze_plate_reader_growth's Introduction

ANALYZE_GROWTH Compute doubling time given kinetic read time series.

Args:
    filename: Full path to kinetic read data. Tab-delimited. First row is
        well names. Each row is the the value of reads at each time point.
    opt_blank_wells: Optional array of wells left blank for calibration.
        Provide as integers. E.g. [48, 96] for wells D12 and H12.
    opt_blank_value: Optional value of blank read. If provided,
        opt_blank_wells is ignored.
    opt_interval: Optional. Interval, in minutes, between reads.
        Default 5 min.
    opt_mid_log_interval: Optional. Size of window, in minutes, for which
        we measure linear growth. Default 40 minutes.
    opt_hide_plots: Optional. Boolean. If true, hide plots.
    opt_output_override: Optional. Override the name of the output file.

The output is written to a new file in the same location as the input
a text file, with extension '.analyzed_growth.csv'. This can be imported
into Excel as a tab-delimited file.

Example usage:

    analyze_growth('/home/glebk/Data/2015_06_10_growth_test.txt')

Blank wells may be provided to be sourced as the average blank read.
For example, if well H12 (96th well) is blank:

    analyze_growth('/home/glebk/Data/2015_06_10_growth_test.txt', [96])

Alternatively, one can provide a global blank value to adjust all reads by:

    analyze_growth('/home/glebk/Data/2015_06_10_growth_test.txt', [], 0.09)

Note for using optional arguments: User must provide values for all
arguments up to the optional argument you would like to use.
For example, to set opt_mid_log_interval to 30 min, the command is:

    analyze_growth('/home/glebk/Data/2015_06_10_growth_test.txt', [], 0, 5, 30)

Authors:
    Jaron Mercer - ported to Matlab
    Harris Wang - original draft
    Gleb Kuznetsov ([email protected]) - primary maintainer
    Tim Wannier

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