plotoRes: Produces optimisation diagnostic plots

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Produces optimisation diagnostic plots

Description

This function takes a combined optimisation list as produced by oRes and plots a number of diagnostic curves to file

Usage

plotoRes(opres, data.On=data.P, optParam=optParam)

Arguments

opres	a list produced by oRes
data.On	a GMMbyCond object, as created by dataBycond (as it was fed into the optimisation)
optParam	an OptParam object with at least elements resN (the index of the optimisation, this is the suffix of the Resultsx.RData files, it will be used to name the pdf file "presN.pdf")

Details

The plots that are produced are: 1. the average of the population and best model size, at each generation; 2.the drug specific scores of the best model of each generation, along generations; 3. the average drug specific scores of the population, along generations; 4. the total best model and population average scores along generations (without size penalty); 5. the total best model and population average scores along generations (with size penalty); 6.the evolution of frequency of edges along generations (1 curve for each edge), separated in 3 categories 6.A. edges that have a final frequency between 0.4 and 0.6, 6.B. edges that have a final frequency above 0.6, and 6.C. edges that have a final frequency below 0.4. Note that all these numbers are computed based on a population size of 5000.

Value

This function doesn't return anything, it just produces plots that are stored in a single pdf file.

Author(s)

C. Terfve

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.