Plot mass spectra — orbi_plot

This function visualizes mass spectra from aggregated raw file data. The spectra have to be be previously read in with include_spectra = c(1, 10, 100) in orbi_read_raw(). By default, this function tries to visualize different isotopcule ranges (monoisotopic peak, M+1, M+2, M+3). To focus only on isotopcules of interest, run orbi_identify_isotopocules() and orbi_filter_isotopocules() first.

Usage

orbi_plot_spectra(
  aggregated_data,
  mz_min = 0,
  mz_max = Inf,
  mz_base_peak = NULL,
  mz_focus_nominal_offsets = 0:4,
  max_scans = 6,
  max_files = 4,
  label_peaks = TRUE,
  show_filenames = TRUE,
  show_ref_and_lock_peaks = TRUE,
  show_focus_backgrounds = TRUE,
  background_colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02",
    "#A6761D", "#666666", "#BBBBBB")
)

Arguments

aggregated_data: data aggregated by orbi_aggregate_raw() and, optionally, with isotopocules already identified by orbi_identify_isotopocules(), and (also optionally), alreadty filtered with orbi_filter_isotopocules()
mz_min: which mz to start the main plot window at. By default include all.
mz_max: which mz to end the main plot window at. By default include all.
mz_base_peak: where is the base peak at (approximately)?. If not specified (the default), takes the largest peak in the mz_min to mz_max window.
mz_focus_nominal_offsets: which panels to visualize? 0 = whole spectrum, 1 = spectrum around monoisotopic peak + 1 mu (M+1), 2 = M+2, etc. By default includes the whole spectrum and up to +1, +2, +3, and +4 peaks (if they exist). To visualize only the whole spectrum, use mz_focus_nominal_offsets = 0. Likewise, to visualize only the area around the monoisotopic peak +1, provide mz_focus_monimal_offsets = 1 (or = c(1, 2) for both +1 and +2 windows).
max_scans: spectra from how many scans to show at most. By default up to 6 (the number of available linetypes). To show only the spectrum from a single scan, set max_scans = 1. If more than 6 scan spectra are allowed (and there are more than 6 loaded in the aggregated_data), turns of the linetype aesthetic.
max_files: spectra from how many files to show at most. Each file is shown as an additional line of panels.
label_peaks: whether to label the peaks in the M+1/2/3 panels. If isotopcules are already identified from orbi_identify_isotopocules(), uses the isotopcule names, otherwise the m/z values. Peaks that are missing (identified by orbi_identify_isotopocules()) in all spectra are highlighted in red. To avoid labeling unidentified/missing peaks, run orbi_filter_isotopocules() first.
show_filenames: whether to show the filename in the first panel of reach row (usually the full spectrum panel)
show_ref_and_lock_peaks: whether to show reference and lock mass peaks in the spectrum
show_focus_backgrounds: whether to highlight the M+x panels with specific background colors that match them with the mass bands highlighted in the first panel
background_colors: the colors to use for the background highlighting