Bio.phenotype.pm_fitting module¶
Growth curves fitting and parameters extraction for phenotype data.
This module provides functions to perform sigmoid functions fitting to Phenotype Microarray data. This module depends on scipy curve_fit function. If not available, a warning is raised.
Functions: logistic Logistic growth model. gompertz Gompertz growth model. richards Richards growth model. guess_plateau Guess the plateau point to improve sigmoid fitting. guess_lag Guess the lag point to improve sigmoid fitting. fit Sigmoid functions fit. get_area Calculate the area under the PM curve.
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Bio.phenotype.pm_fitting.
logistic
(x, A, u, d, v, y0)¶ Logistic growth model.
Proposed in Zwietering et al., 1990 (PMID: 16348228)
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Bio.phenotype.pm_fitting.
gompertz
(x, A, u, d, v, y0)¶ Gompertz growth model.
Proposed in Zwietering et al., 1990 (PMID: 16348228)
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Bio.phenotype.pm_fitting.
richards
(x, A, u, d, v, y0)¶ Richards growth model (equivalent to Stannard).
Proposed in Zwietering et al., 1990 (PMID: 16348228)
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Bio.phenotype.pm_fitting.
guess_lag
(x, y)¶ Given two axes returns a guess of the lag point.
The lag point is defined as the x point where the difference in y with the next point is higher then the mean differences between the points plus one standard deviation. If such point is not found or x and y have different lengths the function returns zero.
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Bio.phenotype.pm_fitting.
guess_plateau
(x, y)¶ Given two axes returns a guess of the plateau point.
The plateau point is defined as the x point where the y point is near one standard deviation of the differences between the y points to the maximum y value. If such point is not found or x and y have different lengths the function returns zero.
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Bio.phenotype.pm_fitting.
fit
(function, x, y)¶ Fit the provided function to the x and y values.
The function parameters and the parameters covariance.
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Bio.phenotype.pm_fitting.
get_area
(y, x)¶ Get the area under the curve.