plotAdjustedRtime: Visualization of alignment results

In xcms: LC-MS and GC-MS Data Analysis

Description

Plot the difference between the adjusted and the raw retention time (y-axis) for each file along the (adjusted or raw) retention time (x-axis). If alignment was performed using the adjustRtime-peakGroups method, also the features (peak groups) used for the alignment are shown.

Usage

plotAdjustedRtime(
  object,
  col = "#00000080",
  lty = 1,
  lwd = 1,
  type = "l",
  adjustedRtime = TRUE,
  xlab = ifelse(adjustedRtime, yes = expression(rt[adj]), no = expression(rt[raw])),
  ylab = expression(rt[adj] - rt[raw]),
  peakGroupsCol = "#00000060",
  peakGroupsPch = 16,
  peakGroupsLty = 3,
  ylim,
  ...
)

Arguments

object	A XCMSnExp object with the alignment results.
col	colors to be used for the lines corresponding to the individual samples.
lty	line type to be used for the lines of the individual samples.
lwd	line width to be used for the lines of the individual samples.
type	plot type to be used. See help on the par function for supported values.
adjustedRtime	logical(1) whether adjusted or raw retention times should be shown on the x-axis.
xlab	the label for the x-axis.
ylab	the label for the y-axis.
peakGroupsCol	color to be used for the peak groups (only used if alignment was performed using the adjustRtime-peakGroups method.
peakGroupsPch	point character (pch) to be used for the peak groups (only used if alignment was performed using the adjustRtime-peakGroups method.
peakGroupsLty	line type (lty) to be used to connect points for each peak groups (only used if alignment was performed using the adjustRtime-peakGroups method.
ylim	optional numeric(2) with the upper and lower limits on the y-axis.
...	Additional arguments to be passed down to the plot function.

Author(s)

Johannes Rainer

See Also

adjustRtime for all retention time correction/ alignment methods.

Examples

## Load a test data set with detected peaks
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

## Disable parallel processing for this example
register(SerialParam())

## Performing the peak grouping using the "peak density" method.
p <- PeakDensityParam(sampleGroups = c(1, 1, 1))
res <- groupChromPeaks(faahko_sub, param = p)

## Perform the retention time adjustment using peak groups found in both
## files.
fgp <- PeakGroupsParam(minFraction = 1)
res <- adjustRtime(res, param = fgp)

## Visualize the impact of the alignment.
plotAdjustedRtime(res, adjusted = FALSE)
grid()

xcms documentation built on Nov. 8, 2020, 5:13 p.m.