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

In 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$All.results)[seq(3, dim(opt$All.results)[2], 1)],
  ...
)

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, intercept=FALSE, check.input=FALSE)
opt<-optimizeParameters(Y, kW.hat=c(1,5,10), nu.hat=c(100,100000), 
nc_index=seq(251,500,1), methods=c("fnorm"), cpus=1, parallel=FALSE)
try(dev.off(), silent=TRUE)
plot(opt, main="Heatmap Plot")

RUVcorr documentation built on Nov. 8, 2020, 5:10 p.m.