Visualize integration boundaries for proteoform ions.

Source: R/visualization.R

This function plots one or several mass spectra overlaid with mass-to-charge ratios and integration boundaries of proteoform ions.

plot_ions(
  ms_data,
  ions,
  scans = NULL,
  rt_limits = NULL,
  xlim = NULL,
  plot_elements = c("mz", "mz_min", "mz_max", "ion_labels"),
  filter_ms1 = TRUE
)

Arguments

ms_data

Mass spectrometry data stored in an mzR object as returned by mzR::openMSfile().
ions

A data frame describing mass-to-charge ratios of proteoform ions as returned by ionize().
scans

Scan numbers to show (vector of integers). If NULL, show all spectra in the file.
rt_limits

A numeric vector with two elements specifying retention time limits (in seconds) for selecting scans. If values are specified for both scans and rt_limits, the function issues a warning and ignores the value of the latter.
xlim

x-axis limits, given as c(lower, upper). If NULL, use the default scale range.
plot_elements

Character vector specifying which plot elements should be displayed:

"mz"

Solid red vertical lines indicating m/z values.

"mz_min", "mz_max"

Dashed red vertical lines indicating lower and upper integration boundaries, respectively.

"ion_labels"

Secondary x-axis, labeled by the names and charges of the proteoform ions shown.
filter_ms1

If true, only scans from MS level 1 are selected by the retention time limits.

Value

A ggplot object describing the created plot.

Examples

ms_data <- mzR::openMSfile(
  system.file("extdata", "mzml", "mab1.mzML", package = "fragquaxi")
)

proteins <- define_proteins(
  system.file("extdata", "mab_sequence.fasta", package = "fragquaxi"),
  .disulfides = 16
)

modcoms <- define_ptm_compositions(sample_modcoms)

pfm_ions <-
  assemble_proteoforms(proteins, modcoms) %>%
  ionize(36L)

# show all scans
plot_ions(ms_data, pfm_ions, xlim = c(4100, 4150))


# show selected scans
plot_ions(ms_data, pfm_ions, scans = 126:136, xlim = c(4100, 4150))


# show a single scan
plot_ions(ms_data, pfm_ions, scans = 126, xlim = c(4100, 4150))


# only show selected plot elements
plot_ions(ms_data, pfm_ions,
          scans = 126, xlim = c(4100, 4150),
          plot_elements = c("mz", "ion_labels"))