# trim by threshold new_peak_list = num_ions_threshold(pl, n, t) print "Number of filtered peaks: ", len(new_peak_list) # TIC from raw data tic = data.get_tic() # save TIC to a file # Get Ion Chromatograms for all m/z channels n_mz = len(im.get_mass_list()) ic = [] for m in range(n_mz): ic.append(im.get_ic_at_index(m)) # Create a new display object, this time plot the ICs # and the TIC, as well as the peak list display = Display() display.plot_tic(tic, 'TIC') display.plot_ics(ic) display.plot_peaks(new_peak_list, 'Peaks') display.do_plotting('TIC, and PyMS Detected Peaks')
# determine and set area area = peak_sum_area(im, peak) peak.set_area(area) # print some details UID = peak.get_UID() # height as sum of the intensities of the apexing ions height = sum(peak.get_mass_spectrum().mass_spec) print UID + ", %.2f, %.2f, %.2f" % (rt, height, peak.get_area()) # TIC from raw data tic = data.get_tic() # baseline correction for TIC tic_bc = tophat(tic, struct="1.5m") # Get Ion Chromatograms for all m/z channels n_mz = len(im.get_mass_list()) ic = [] for m in range(n_mz): ic.append(im.get_ic_at_index(m)) # Create a new display object, this time plot the ICs # and the TIC, as well as the peak list display = Display() display.plot_tic(tic_bc, 'TIC BC') display.plot_ics(ic) display.plot_peaks(new_peak_list, 'Peaks') display.do_plotting('TIC, and PyMS Detected Peaks')
# trim by relative intensity pl = rel_threshold(peak_list, r) # trim by threshold new_peak_list = num_ions_threshold(pl, n, t) print "Number of filtered peaks: ", len(new_peak_list) # TIC from raw data tic = data.get_tic() # save TIC to a file # Get Ion Chromatograms for all m/z channels n_mz = len(im.get_mass_list()) ic = [] # All plotting from here on for m in range(n_mz): ic.append(im.get_ic_at_index(m)) # Create a new display object, this time plot the ICs # and the TIC, as well as the peak list display = Display() display.plot_tic(tic, 'TIC') display.plot_ics(ic) display.plot_peaks(new_peak_list, 'PyMS peaks') display.do_plotting()