Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:31Z

Mtrevisan: Created page with "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 l..."

2017-10-03T14:22:11Z

Created page with "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 l..."

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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=" ".

← Older revision		Revision as of 14:17, 19 February 2018
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	--ylabel=string Use the selected string for the Y label. Default is		--ylabel=string Use the selected string for the Y label. Default is
	"Rank/N". To remove the label, use --ylabel=" ".		"Rank/N". To remove the label, use --ylabel=" ".
		+
		+	[[Category:SanXoT software package]]

SanXoTGauss - Revision history

Mtrevisan at 14:17, 19 February 2018

Mtrevisan: Created page with "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 l..."