SanXoTGauss

SanXoTgauss v0.22 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to depict the sigmoids of lower level elements compared to their higher levels. For example: when integrating proteins into categories, the outStats from the protein confluence will be used along with a list of categories to compare the sigmoid representing the proteins of each category.

SanXoTgauss needs three input files:

• a stats file, the outStats file from SanXoT (using the -z command)
• a higher level list to graph (using the -c command)
• a relations file (using -r command)

And delivers four output file:

• the data file used to draw gaussians (default suffix: "_outSigmoids")
• an extra table with a different arrangement of the previous one (default suffix: "_extraTable")
• the graph (default suffix: "_outGraph")
• the log file (default suffix: "_logFile")

Usage:

sanxotgauss.py -z[stats file] -r[relations file] -c[higher level list file] [OPTIONS]

Arguments:

  -h, --help          Display this help and exit.
  -a, --analysis=string
                      Use a prefix for the output files. If this is not
                      provided, then the prefix will be garnered from the
                      stats file.
  -c, --list=filename The text file containing the higher level elements whose
                      sigmoids we want to graph. If the first element is not
                      taken, it might help saving the file with ANSI format.
  -d, --graphdpi=integer
                      Set a non-default graph size in dpi (dots per inch).
                      Default is 300 dpi.
  -g, --no-graph      Do not show the sigmoids graph (the file will be saved
                      in any case).
  -G, --outgraph=filename
                      To use a non-default name for the graph file.
  -k, --no-legend     Do not show the legend in the graph (useful when the
                      legend covers the graph, in which case we might want to
                      save it twice: one with legend, and again without it).
  -l, --graphlimits=integer
                      To set the +- limits of the Zij graph (default is 6). If
                      you want the limits to be between the minimum and
                      maximum values, you can use -l.
  -L, --logfile=filename
                      To use a non-default name for the log file.
  -o, --outputfile=filename
                      To use a non-default file name for the sigmoid table.
  -p, --place, --folder=foldername
                      To use a different common folder for the output files.
                      If this is not provided, the the folder used will be the
                      same as the stats file folder.
  -r, --relfile, --relationsfile=filename
                      Relations file, with identificators of the higher level
                      in the first column, and identificators of the lower
                      level in the second column.
  -s, --graphfontsize=float
                      Use a non-default value for legend font size. Default
                      is 8.
  -t, --graphtitle=string
                      The graph title (default is "Z plot").
  -T, --minimalgraphticks
                      It will only show the x secondary line for x = 0, and
                      none for the Y axis (useful for publishing).
  -W, --graphlinewidth=float
                      Use a non-default value for the sigmoid line width.
                      Default is 1.0.
  -x, --extratable=filename
                      To use a non-default file name for the extra table.
  -z, --outstats=filename
                      The outStats file from a SanXoT integration.
  -Z, --labelfontsize=float
                      The font size used for the labels in the X and Y axes.
                      (Default is 12.)
  --xlabel=string     Use the selected string for the X label. Default is
                      "Zij". To remove the label, use --xlabel=" ".
  --ylabel=string     Use the selected string for the Y label. Default is
                      "Rank/N". To remove the label, use --ylabel=" ".