peaks.results.plot: likeLTD::peaks.results.plot

Description Usage Arguments Details Value See Also Examples

View source: R/maximize-peaks.R

Description

Plot distribution of fitted peaks along with actual peak heights.

Usage

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peaks.results.plot(hyp,res,replicate=1,toplot=NULL,fileName=NULL,...)

Arguments

hyp

Hypothesis used to generate parameters for optimisation.

res

Either prosecution or defence results from evaluate.peaks e.g. results$Pros or results$Def.

replicate

Which replicate results to plot.

toplot

Integer vector indicating which loci to plot. If NULL, all loci are plotted.

fileName

Output file name for plot. If NULL the plot is output to a plot window instead.

...

Extra parameters to pass to boxplot.

Details

CSP peak heights for a single replicate are plotted, with boxplots representing the distribution for each peak height estimated through optimisation.

Value

Pdf file or plot window.

See Also

plot.CSP.heights

Examples

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## Not run: 
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"laboratory")

# File paths and case name for allele report
admin = pack.admin.input.peaks(
            peaksFile = file.path(datapath, 'laboratory-CSP.csv'),
            refFile = file.path(datapath, 'laboratory-reference.csv'),
            caseName = "Laboratory",
            detectionThresh = 20
             )

# Enter arguments
args = list(
        nUnknowns = 1
        )

# Create hypotheses
hypP = do.call(prosecution.hypothesis.peaks, append(admin,args))
hypD = do.call(defence.hypothesis.peaks, append(admin,args))

# Get parameters for optimisation
paramsP = optimisation.params.peaks(hypP)
paramsD = optimisation.params.peaks(hypD)

# reduce number of iterations for demonstration purposes
paramsP$control$itermax=25
paramsD$control$itermax=25

# Run optimisation
# n.steps and converge set for demonstration purposes
results = evaluate.peaks(paramsP, paramsD, n.steps=1, 
      converge=FALSE)

# plot fitted results under prosecution
peaks.results.plot(hypP,results$Pros)

# plot fitted results under defence
peaks.results.plot(hypD,results$Def)

# plot fitted results for first four loci
peaks.results.plot(hypP,results$Pros,toplot=1:4)

## End(Not run)

likeLTD documentation built on May 1, 2019, 7:58 p.m.