PeakInspector-help.txt

PEAKINSPECTOR HELP

- When running "python PeakInspector.py" from the terminal, the script will read the information about the graphical 
  representation from a file called PeakInspector.ini contained in the "config/" folder. In case you want to enter the 
  information through the graphical user interface (instead of with the PeakInspector.ini file) the 
  script should be executed as follows: "python PeakInspector.py -gui".


- Running it in the latter way will open a small interface in which it should be indicated:
    1) Number of graphs to be plotted.
    2) File with the histogram generated by PeakModeller.py.
    3) Optionally, you can specify a file with the masses that will be represented in the graphs as vertical lines. 
       This file must contain a column "DM" with the delta masses and, optionally, a second column "Name" with a 
       name associated to each delta mass.


- Then, the following information must be indicated for each of the graphs to be represented:
    1) X: Column represented on the abscissa axis. Normally, the column selected in this case will be "midpoint", 
       which contains the midpoint of the bins for each delta mass.
    2) Y: Column represented on the ordinate axis (can be more than one). For example, 
       if the "count" column is selected, the plot will show a histogram with the number of PSMs associated to each delta mass.
    3) Line/Scatter: You can select whether the histogram will be represented by a continuous line (Line) 
       or by a point cloud (Scatter).
    4) Threshold: The values assigned to threshold will be represented in the plot as a horizontal line
       with Y equal to the indicated value.


- By clicking on "Plot", the graphs will be displayed in the browser. In addition, a .HTML file 
  with the plots will be saved in the same folder where the input file with the data was located.