plotGroup: Plot profiles for each peak group

In ChiungTingWu/ncGTW: Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

Description

This function plots sample profiles with loaded information.

Usage

plotGroup(ncGTWinput, sampleRt,
  sampleInd = seq_len(dim(ncGTWinput@rtRaw)[1]), ind = NULL,
  savePath = NULL, show = TRUE, sub = TRUE, filter = FALSE)

Arguments

ncGTWinput	An object return by loadProfile of sample profiles for plotting.
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 1:dim(ncGTWinput$rtRaw)[1].
ind	A user defined index, and the default is NULL.
savePath	The path to save the plots, and the default is NULL (do not save anything).
show	Show the plot in R or not, and the default is TRUE.
sub	Show more information on the plot or not, and the default is TRUE.
filter	Apply a Gaussian filter for demonstration or not, and the default is FALSE.

Details

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.

Value

A plot to the current device.

Examples

# 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)

ChiungTingWu/ncGTW documentation built on Dec. 30, 2019, 10:12 p.m.