Visualization of Alignment Results

The plotAdjustedRtime function plots the difference between the adjusted and raw retention times on the y-axis against the raw retention times on the x-axis. Each line represents the results for one sample (file). If alignment was performed using the peak groups method (see adjustRtime() for more infromation) also the peak groups used in the alignment are visualized.

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 XcmsExperiment() or XCMSnExp() object with the alignment results.

col

color(s) for the individual lines. Has to be of length 1 or equal to the number of samples.

lty

line type for the lines of the individual samples.

lwd

line width for the lines of the individual samples.

type

plot type (see par() for options; defaults to type = "l").

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 if alignment was performed using the peak groups method.

peakGroupsPch

point character (pch) to be used for the peak groups (only if alignment was performed using the peak groups method.

peakGroupsLty

line type (lty) to be used to connect points for each peak groups (only if alignment was performed using the peak groups method.

ylim

optional numeric(2) with the upper and lower limits on the y-axis.b

...

Additional arguments to be passed down to the plot function.

Author

Johannes Rainer

Examples

## Load a test data set with detected peaks
faahko_sub <- loadXcmsData("faahko_sub2")

## 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)
#> Performing retention time alignment using 19 anchor peaks.
#> Warning: Span too small for 'loess' and the available number of peak groups, resetting to 0.21
#> Warning: Adjusted retention times had to be re-adjusted for some files to ensure them being in the same order than the raw retention times. A call to 'dropAdjustedRtime' might thus fail to restore retention times of chromatographic peaks to their original values. Eventually consider to increase the value of the 'span' parameter.

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