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designGG (version 1.1)

plotAllScores: Plot scores profiles

Description

Plot all scores and the temperature at each iteration during the simulated annealing process.

Usage

plotAllScores(plot.obj,fileName=NULL)

Arguments

plot.obj
a list containing: scores, cooling, startTemp, temperature, temperature.step, nIterations and optimality. Details can be found below. scores: A- or D- optimality score of all accepted designs during optimization process. cooling: describes the cooling step in the Simulated Annealing, defined as (new.score $-$ now.score)/ now.score. startTemp:starting temperature of the simulated annealing process. temperature:final temperature that the simulated annealing reaches. temperatureStep:temperature decreasing step in the simulated annealing (SA) process. nIterations:number of iterations in the simulated annealing method. optimality:type of optimality, i.e. "A" (A-optimality) or "D" (D-optimality). A-optimality minimizes $Trace((X'X)^-1)$, which corresponds to minimum average variance of the parameter estimates. D-optimality minimizes $det(X'X)^-1$, which corresponds to minimum generalized variance of the parameter estimates.
fileName
the final optimal design table(s) in csv format and a plot (in png format) of the all scores during SA process (if plotScores = TRUE) will be produced. The users can specify the table and plot name by setting fileName. If NULL (default) it produces files starting with "myDesignGG".

Value

Draw a plot that visualizeds the scores (y-axis) at each iteration during the simulated annealing process (x-axis is time of moving)

References

Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical genomics: the added value from environmental perturbation, Trends Genet (2008) 24:518-524. Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen. designGG: An R-package and Web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics 10:188(2009) http://gbic.biol.rug.nl/designGG

Examples

Run this code
    data(examplePlotObj)
    plotAllScores(examplePlotObj) 

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