Skewnormal Curve fitting

Set of routines to fit dose-response data to a skewnormal CDF (cummulative distribution function) curve. The resultant curve fit produces three parameters:

• a: a measure of distribution skew.
  • a negaive value of a will have the distribution skewing to the left
  • a positive value of a will have the distribution skewing to the right
• loc: parameter specifying the center of the distribution (x axis)
• scale: parameter specifying the spread of the distribution (x axis)

Processing of datasets

Processing of data is in file skewnormal_dr_curve_fit.py.
It is not part of the library itself but retrieves data and calls the library functions. This calling module

• reads a file (either Tox21 or PubCHem dataset) and iterates through each molecule endpoint, extracting molecule identification information, dose and response data as well as Hill equation parameters, Hill coefficient and AC50.

For each molecule:

• the log10 of the response data is taken, scaled between zero and one and then the curve fittling routine is called.
• if the curve fit is successful the dose response data is plotted, along with the curve fit to the skewnormal CDF and the Hill equation using paraaeters provided in the data file; this file is saved.
  • for the comparison plot the fitted curves (skewnormal CDF and Hill) are reverse scaled so that they can be compared to the unprocessed dose response data.
• all of the extracted information about each molecule, as well as the skewnormal and Hill equation parameters, are put into a dictionary that is exposrted to a JSON file.

Methods and files

Processing data

data_processing.py

• retrieve_data_metrics
• scale_response
• restore_response
• hill_eqn
• inv_hill_eqn

Curve fitting routines

curve_fit.py

• func_skewnorm_cdf
• find_skewnorm_curve_parameters
• analyze_dose_response
• successful_skewnorm_curvefit

Distibution plotting routines

plot_curves.py

• plot_skewnorm
• plot_skewnorm_curve_fit
• plot_hill_eqn
• plot_skewnorm_hill