maldi_draw_peaks_by_well: Draw m/z peaks in spectra

In benjbuch/summerrmass: Measure and Analyze MALDI Peaks

Description

Draws spectra and places them on a pdf page for printing.

Usage

maldi_draw_peaks_by_well(
  object,
  data_peaks,
  ncol = 2,
  nrow = 6,
  highlight_missing_peaks = TRUE,
  title = NULL,
  SNR = NULL
)

Arguments

object	A (list of) MassSpectrum.
data_peaks	A peak data table as returned by maldi_find_peaks_by_well; must be a subset of object.
ncol	Number of plot columns to arrange per page.
nrow	Number of plot rows to arrange per page.
highlight_missing_peaks	Whether or not spectra in which not all peaks are detected should be highlighted.
title	Optional title of plot.
SNR	Optional signal-to-noise level used to detect peaks.

Details

No checking is done whether data_peaks was indeed derived from object. However, data_peaks must contain a column findex which points to the index of corresponding spectrum in object.

Examples

data("BobCAT")

my_masses <- c(ion_species_A = 2425, ion_species_B = 2441)

# trim the spectra during averaging to speed-up the peak detection; alternatively
# use MALDIquant::trim(...).
my_spectrum <- maldi_average_by_well(BobCAT, final_trim_range = c(2420, 2445))
# detect peaks at the masses
my_peaks <- maldi_find_peaks_by_well(my_spectrum, my_masses)

benjbuch/summerrmass documentation built on Dec. 19, 2021, 8:43 a.m.