plotAdjustedRtime: Visualization of Alignment Results

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

Visualization of Alignment Results

Description

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(s)

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)

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

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.