plotAdjustedRtime: Visualization of alignment results

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Visualization of alignment results

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

## Below we perform first a peak detection (using the matchedFilter
## method) on some of the test files from the faahKO package followed by
## a peak grouping and retention time adjustment using the "peak groups"
## method
library(faahKO)
library(xcms)
fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
           full.names = TRUE)

## Reading 2 of the KO samples
raw_data <- readMSData(fls[1:2], mode = "onDisk")

## Perform the peak detection using the matchedFilter method.
mfp <- MatchedFilterParam(snthresh = 20, binSize = 1)
res <- findChromPeaks(raw_data, param = mfp)

## Performing the peak grouping using the "peak density" method.
p <- PeakDensityParam(sampleGroups = c(1, 1))
res <- groupChromPeaks(res, 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. We show both versions of the plot,
## with the raw retention times on the x-axis (top) and with the adjusted
## retention times (bottom).
par(mfrow = c(2, 1))
plotAdjustedRtime(res, adjusted = FALSE)
grid()
plotAdjustedRtime(res)
grid()

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.