Associated Scripts for FTMS Ionisation Sources Comparisons
All scripts are shared with the same license as the rest of this repository. This is the GNU GPLv3 License.
File 0-SpectrumPlotter.py loads in raw Bruker SolariX fids and plots them using the Spike package.
File 1-Process-Data.py reads in the data assigned by Formularity and reprocesses it for ease with other scripts.
File 1-Process-Data-Part2.py does a similar thing but outputs the data in groups (by ionisation source).
File X-CombinedNegative.py reads in deprotonated and radical assignments from Formularity and generates a single, combined output. It does not have a conflict resolution method as this was not required in this instance.
The various 'HitCollator' files collate the assignments for several statistics to be calculated, i.e. mass errors, number of radicals, or just overall information.
File 4-DataVisualisation.py produces panel plots in the form of van krevelen, DBE vs C number, or AImod vs C number plots.
File 4-DataVisualisation-HeteroClass.py produces two types of heteroatomic class plots.
File 4-DataVisualisation-Uniques.py produces van Krevelen and DBE plots of the unique formula for each ionisation source in one plot.
File 4-DataViz-Errors.py produces mass error distribution plots.
File 5-DataIntersections.py uses the PyUpSet package to calculate intersections of assignments and produce UpSet plots. The main source of PyUpSet was modified and is provided in visualisation.py for some aesthetic and practical improvements.
File 6-InteractiveVanKrevelens.py produces interactive van krevelen diagrams based on the Bokeh package, and requires the template files to be present in the output directory.
Many of these scripts contain significant sections of commented out code. This was for development and is included for posterity or reference. The scripts should be self-sufficient and run without modification (beyond the obvious pre-requisite of having the relative paths correct)