plotRtmsSample: Plot an RTMS sample object

In rtms: R Toolkit for Mass Spectrometry

Plot an RTMS sample object

Description

plotRtmsSample() takes an RTMS sample object and produces a ggplot object depicting all extracted peaks, and their context windows if included.

Usage

plotRtmsSample(sample, usePeakNames = TRUE, freey = TRUE)

Arguments

sample	An object of class rtmsSample.
usePeakNames	If the list of peaks used to create the sample was a named list, then setting this to TRUE (the default) will use those names to label the facets of the plotted sample. If set to FALSE, the facets will be labelled with the m/z values of each peak. This parameter will be ignored if the peaks are unnamed.
freey	If TRUE (the default) the y-axes of each peak's facet will be allowed to vary freely, so different peaks will be plotted on different scales. Setting this to FALSE will fix all peaks with in a sample on the same y-axis scale.

Value

A ggplot object depicting the RTMS sample.

Examples

peaks <- rtmsPeakList(c(1516.83,1530.84),peakWidth=0.2,windowWidth = c(5,10))
names(peaks) <- c("Product","Substrate")
sample <- getSample(exampleSpectrum,peaks)

plot1 <- plotRtmsSample(sample)
plot2 <- plotRtmsSample(sample,freey=FALSE)

rtms documentation built on June 7, 2023, 5:59 p.m.