Description Usage Arguments Value Examples
These functions plot the deconvoluted spectra and fragment assignments
spectrum.plot.generic plots the deconvoluted peak list as a mass spectrum
spectrum.plot plots the deconvoluted peak list as a mass spectrum
spectrum.label.plot adds fragment assignment labels to spectrum.plot
spectrum.theme.simple modifies the spectrum plot to use black axis labels and no background
1 2 3 4 5 6 7 8 9 | spectrum.plot.generic(mass, intensity, massrange = c(0, Inf),
color = "#000000")
spectrum.plot(data, massrange = c(0, Inf), color = "#000000")
spectrum.label.plot(data, massrange = c(0, Inf), unicode = TRUE,
unassigned = TRUE, mz = FALSE)
spectrum.theme.simple(base_size = 12)
|
mass |
mass vector for generic plotting |
intensity |
intensity vector for generic plotting |
massrange |
a vector describing the lower and upper bounds of the mass range to plot |
color |
the color to use for unlabeled peaks |
data |
output from read.bupid |
unicode |
allow unicode characters in labels |
unassigned |
display unassigned peaks behind the labelled spectrum |
mz |
TRUE to plot in m/z, otherwise mass |
base_size |
base text size for axis labels |
Returns the ggplot object
Returns the ggplot object
Returns the ggplot object
Returns the ggplot object
Returns the ggplot theme
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Not run:
server <- "http://bupid.bumc.bu.edu/cgi-bin/get_results.cgi"
infile <- "key=WBNqTswT5DPg3aDO&ID=320&date=20150309"
data <- read.bupid(url=paste(server,infile,sep="?"))
# plot the entire spectrum
spectrum.plot(data)
# plot peaks between 500 Da and 600 Da with labeled assignments
spectrum.label.plot(data,c(500,600))
# again with a simple theme
spectrum.label.plot(data,c(500,600)) + spectrum.theme.simple()
## End(Not run)
|
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