Chromatogram visualization
In case you need a demo data file.
Base peak chromatogram
Visualize the base peak chromatogram for a raw file:
from masscube import read_raw_file_to_obj
file_name = "demo_data.mzML" # load the raw file
d = read_raw_file_to_obj(file_name) # read the raw file into a MassCube object
# plot the base peak chromatogram
d.plot_bpc()Example output 1
Set more parameters to customize the plot:
from masscube import read_raw_file_to_obj
file_name = "demo_data.mzML" # load the raw file
d = read_raw_file_to_obj(file_name) # read the raw file into a MassCube object
# plot the base peak chromatogram
time_range = (1, 2) # set the time range for the x-axis
label_name = False # do not show file name in the plot
output_dir = None # set the absolute path to save the plot, or None to show it
d.plot_bpc(
time_range=time_range,
label_name=label_name,
output_dir=output_dir
)Example output 2
Extracted ion chromatogram
Plot the extracted ion chromatogram (EIC) for a specific m/z value:
from masscube import read_raw_file_to_obj
d = read_raw_file_to_obj("demo_data.mzML")
# parameters for extracting EICs
target_mz_arr = 138.0521 # m/z value of the target ion. You can also make a list of m/z values, e.g. [138.0521, 150.1234] for
# overlapping EICs
target_rt = 1.774 # target retention time in minutes. Set it to None to plot the whole retention time range
mz_tol = 0.005, # m/z tolerance in Da
rt_tol = 0.3, # retention time tolerance in minutes
rt_range = (1,2), # custom retention time range, e.g. (1, 2) to plot EICs in the range of 1 to 2 minutes
output_file_name = None, # set the absolute path of the output file, or None to show the plot
show_target_rt = True, # dashed blue line at the target retention time
ylim = None, # custom y-axis limits, e.g. [0, 10000]
return_eic_data = False # return the EIC data as a pandas DataFrame
# If True, a list of EIC data: [[eic_time_arr, eic_signals, eic_scan_idx], ...] will be returned
# example 1
d.plot_eics(target_mz_arr=target_mz_arr, target_rt=target_rt)
# example 2
d.plot_eics(target_mz_arr=target_mz_arr, target_rt=target_rt, mz_tol=mz_tol, rt_tol=rt_tol,
rt_range=rt_range, output_file_name=None, show_target_rt=True, ylim=None,
return_eic_data=False)Example output 1
Example output 2
