highlightChromPeaks {xcms} | R Documentation |
The highlightChromPeaks
function adds chromatographic
peak definitions to an existing plot, such as one created by the
plot
method on a Chromatogram
or
Chromatograms
object.
highlightChromPeaks(x, rt, mz, peakIds = character(), border = rep("00000040", length(fileNames(x))), lwd = 1, col = NA, type = c("rect", "point", "polygon"), whichPeaks = c("any", "within", "apex_within"), ...)
x |
For |
rt |
For |
mz |
|
peakIds |
|
border |
colors to be used to color the border of the rectangles/peaks.
Has to be equal to the number of samples in |
lwd |
|
col |
For |
type |
the plotting type. See |
whichPeaks |
|
... |
additional parameters to the |
Johannes Rainer
## Read some files from the faahKO package. library(xcms) library(faahKO) faahko_3_files <- c(system.file('cdf/KO/ko16.CDF', package = "faahKO"), system.file('cdf/KO/ko18.CDF', package = "faahKO")) od <- readMSData(faahko_3_files, mode = "onDisk") ## Peak detection using the 'matchedFilter' method. Note that we are using a ## larger binSize to reduce the runtime of the example. xod <- findChromPeaks(od, param = MatchedFilterParam(binSize = 0.3, snthresh = 20)) ## Extract the ion chromatogram for one chromatographic peak in the data. chrs <- chromatogram(xod, rt = c(2700, 2900), mz = 335) plot(chrs) ## Extract chromatographic peaks for the mz/rt range (if any). chromPeaks(xod, rt = c(2700, 2900), mz = 335) ## Highlight the chromatographic peaks in the area ## Show the peak definition with a rectangle highlightChromPeaks(xod, rt = c(2700, 2900), mz = 335) ## Color the actual peak highlightChromPeaks(xod, rt = c(2700, 2900), mz = 335, col = c("#ff000020", "#00ff0020"), type = "polygon")