This script plots mass spectral data in a 2-D heatmap.
Python2 is deprecated. We follows the trend so this script requires python version >= 3.0. In addition, below external dependency python libraries are also required:
numpy
matplotlib
They must be pre-installed. The easiest way to install them is probably using
pip from command-line (or called terminal):
pip install numpy matplotlib # for Linux/MacOS
On Windows, the above command also works but only after some extra efforts in configuring the environment. Also note that on Windows python is not natively installed; one may find it necessary to download and install python first.
The script needs to be executed from command-line interface (CLI), e.g. in a terminal. A simple example may look like:
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra.mzdata.xml.png
This will plot the data in spectra.mzdata.xml and save into a png image.
The argument option format follows the Linux convention.
./plot_mass_spectra_2d.py --help will show all available options and their
acceptable value format.
The input spectra filename. The file is expected to be in mzdata xml format. Note if the filename includes and special character (anything other than alphabetical (a-z and A-Z) digits (0-9) and underscore (_)), it must be wrapped in quote marks. For example:
./plot_mass_spectra_2d.py spectra mzdata.xml -p spectra.png # NOT ok
./plot_mass_spectra_2d.py "spectra mzdata.xml" -p spectra.png # ok
These two arguments select the time range for plotting, for example:
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra.mzdata.xml.png --from-time 5 --till-time 30
will plot the data between 5-30 min range. By default (if these arguments are not set) the whole range will be plotted
These two arguments select the M/Z range for plotting, for example:
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra.mzdata.xml.png --mz-min 200 --mz-max 1000
will plot the data between 200-1000 M/Z range. The default is 0-1000.
To provide a title for the figure. If not set, the input mzdata xml filename will be used. Note if the title includes and special character (anything other than alphabetical (a-z and A-Z) digits (0-9) and underscore (_)), it must be wrapped in quote marks. For example:
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra.mzdata.xml.png --title my title # NOT ok
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra.mzdata.xml.png --title "my title" # ok
Set output image resolution. default is 300; common values are 72, 100, 150, 300, 600.
Set the output file name. If the filename includes and special character (anything other than alphabetical (a-z and A-Z) digits (0-9) and underscore (_)), it must be wrapped in quote marks. For example:
./plot_mass_spectra_2d.py spectra.mzdata.xml -p spectra plot.png # NOT ok
./plot_mass_spectra_2d.py spectra.mzdata.xml -p "spectra plot.png" # ok