spectrum.plot: Plot spectra

Description Usage Arguments Value Examples

Description

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

Usage

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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)

Arguments

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

Value

Returns the ggplot object

Returns the ggplot object

Returns the ggplot object

Returns the ggplot object

Returns the ggplot theme

Examples

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## 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)

heckendorfc/BTDR documentation built on May 17, 2019, 3:20 p.m.