| plotGroup {ncGTW} | R Documentation |
This function plots sample profiles with loaded information.
plotGroup(ncGTWinput, sampleRt, sampleInd = seq_len(dim(ncGTWinput@rtRaw)[1]), ind = NULL, savePath = NULL, show = TRUE, sub = TRUE, filter = FALSE)
ncGTWinput |
An object return by |
sampleRt |
A list of the same length as the sample number in which each element is a vector corresponding to the sample raw/adjusted RT for plotting. |
sampleInd |
Indicate which samples should be plotted, and the default is
|
ind |
A user defined index, and the default is |
savePath |
The path to save the plots, and the default is |
show |
Show the plot in R or not, and the default is |
sub |
Show more information on the plot or not, and the default is
|
filter |
Apply a Gaussian filter for demonstration or not, and the
default is |
This function plots the extracted ion chromatogram obtained by
loadProfile. The user can decide to save the figure, show the
figure, or apply a Gaussian filter on the data by parameter setting.
A plot to the current device.
# obtain data
data('xcmsExamples')
xcmsLargeWin <- xcmsExamples$xcmsLargeWin
xcmsSmallWin <- xcmsExamples$xcmsSmallWin
ppm <- xcmsExamples$ppm
# detect misaligned features
excluGroups <- misalignDetect(xcmsLargeWin, xcmsSmallWin, ppm)
# obtain the paths of the sample files
filepath <- system.file("extdata", package = "ncGTW")
file <- list.files(filepath, pattern="mzxml", full.names=TRUE)
tempInd <- matrix(0, length(file), 1)
for (n in seq_along(file)){
tempCha <- file[n]
tempLen <- nchar(tempCha)
tempInd[n] <- as.numeric(substr(tempCha, regexpr("example", tempCha) + 7,
tempLen - 6))
}
# sort the paths by data acquisition order
file <- file[sort.int(tempInd, index.return = TRUE)$ix]
# load the sample profiles
ncGTWinputs <- loadProfile(file, excluGroups)
# plot all loaded features
for (n in seq_along(ncGTWinputs))
plotGroup(ncGTWinputs[[n]], slot(xcmsLargeWin, 'rt')$corrected)