LoBrA (version 1.0)

plotLDOScreening: Plotting the screening results.

Description

For each peak two box plots are created. The first plot shows a boxplot of the Sample Intercept Comparison of the sample and the background, and the corresponding p-values. The second plot shows a boxplot of the Residual Comparison of the sample and the background, and the corresponding p-values.

Usage

plotLDOScreening(
  ldoscreen,
  plotAll = FALSE,
  correctionmethod = "levene",
  decs = 3,
  ask = FALSE,
  peaknames = rownames(ldoscreen@selectedPeaks)
)

Arguments

ldoscreen

LDO screening result

plotAll

Select all components to be plotted. Default plots only the selected peaks using the correction method.

correctionmethod

Version of correction method to be used to select the peaks. Valid values are 'bf', 'levene', and 'bartlett'.

decs

decimal numbers of p-values to be plotted.

ask

logical. Modifies the graphical parameter ask in par (If TRUE (and the R session is interactive) the user is asked for input, before a new figure is drawn. As this applies to the device, it also affects output by packages grid and lattice. It can be set even on non-screen devices but may have no effect there.)

peaknames

Defining a list of peaks to be plotted. By default all peaks will be plotted.

Value

No return value

Examples

# NOT RUN {
# }
# NOT RUN {
  wd <- tempdir()
  data(LoBraExample)
  ldos<-screening(ldo, method= c('levene'), alpha =0.05, criteria=c(1,1))
  filename<- file.path(wd, "screeningresults.pdf") 
  grDevices::pdf(filename, width=16, height=8)
  plotLDOScreening(ldos)
  grDevices::dev.off();

# }