plot.optimizeParameters: Plots an object of class 'optimizeParameters'.

In PeteHaitch/RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis.

Description

plot.optimizeParameters generates a heatmap of the quality assessment values stored in the object of class optimizeParameters .

Usage

## S3 method for class 'optimizeParameters'
plot(x,
  main = colnames(opt$All.results)[3:dim(opt$All.results)[2]], ...)

Arguments

x	An object of the class optimizeParameters.
main	A character string describing title of plot.
...	Further arguments passed to or from other methods.

Details

The black point in the heatmap denotes the optimal parameter combination.

Value

plot.optimizeParameters returns a plot.

Author(s)

Saskia Freytag

See Also

optimizeParameters

Examples

Y<-simulateGEdata(500, 500, 10, 2, 5, g=2, Sigma.eps=0.1, 250, 100, check.input=FALSE)
# This calculation may take a couple of minutes (if possible change number of cpus used)
opt<-optimizeParameters(Y, kW.hat=c(1,5,10), nu.hat=c(100,100000),
nc_index=251:500, methods=c("fnorm"), cpus=1, parallel=FALSE)
try(dev.off(), silent=TRUE)
plot(opt, main="Heatmap Plot")

PeteHaitch/RUVcorr documentation built on May 8, 2019, 1:31 a.m.