Sanson - Revision history

Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:26Z

Mtrevisan: Sanson v1.11 with more graph options, useful for publishing: minfontsize, maxfontsize, graphdpi and graphratio.

2017-11-13T11:01:51Z

Sanson v1.11 with more graph options, useful for publishing: minfontsize, maxfontsize, graphdpi and graphratio.

Mtrevisan: Created page with "Sanson v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the similarity graph..."

2017-10-03T14:19:57Z

Created page with "Sanson v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the similarity graph..."

New page

Sanson v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the similarity graph of a set of categories.

A similarity graph is a graph that shows the relationship between a set of categories by taking into account how many proteins they share. This is measured with a variable f such that for categories c1 and c2, we get:

f(c1, c2) = (#proteins shared by c1 and c2) / (#proteins of c1)

for instance:
:* if c1 == c2, we get f(c1, c2) = f(c2, c1) = 1;
:* if c1 and c2 do not share any proteins, we get f(c1, c2) = f(c2, c1) = 0;
:* if c2 is contained in c1, we get f(c1, c2) <= 1, f(c2, c1) = 1, etc

If no f number is given with the parametres (-e), then the program automatically calculates the best f number, by maximising both the number of category clusters and the number categories within each cluster.

Sanson 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 five output files:

:* the graph in PNG format (default suffix: "_simGraph.png")
:* the DOT language text file used to generate the graph (default suffix: "_simGraph.gv")
:* a table showing the clusters generated (default suffix: "_outClusters")
:* the similarity matrix used to generate the graph (default suffix: "_outSimilarities")
:* a log file (default suffix: "_logFile")

Usage:
sanson.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.
-b, --nosubstats To avoid colouring the boxes according to the proteins
that are in the concerning category (in this case, the
box is coloured using the Zij of the category, when this
information is available in the higher level list to
graph, see -c command).
-c, --list=filename The text file containing the higher level elements whose
categories we want to relate. If the first element is
not taken, it might help saving the file with ANSI
format. If a header is used, then it must be in the form
"id>n>Z>FDR" or "id>Z>n" (where ">" means "tab").
-d, --dotfile=filename
To use a non-default name for the text file in DOT
language, which is used to generate the graph.
-e, --similarity=float
To override the calculation of the optimal f number (see
above for more details).
-g, --graphformat=string
File format for the similarity graph (default is "png").
-G, --outgraph=filename
To use a non-default name for the graph file.
-l, --graphlimits=integer
To set the +- limits of the most intense red/green
colours in the graph (default is 6).
-L, --logfile=filename
To use a non-default name for the log file.
-m, --simfile=string
To use a non-default name for the similarity matrix
file.
-N, --altmax=integer
Maximum number of lower level elements that the alt text
of the higher level node will show per side. For
instance, for N = 3, alt text will show all the elements
up to six; beyond this, only the first and last three
will be shown. (Default is N = 5.) (Note that this will
have effect if the SVG format is used.)
-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, --outcluster=filename
To use a non-default name for the file containg the
list of clusters.
-z, --outstats=filename
The outStats file from a SanXoT integration.

--nonparetoopacity=float
To "downlight" nodes not part of the Pareto front.
(default = 0.5, 0.0 means node color = background,
1.0 means no difference between Pareto front and
non-Pareto font)

--selectednodecolor=#rrggbb, --selectednodecolour=#rrggbb
--defaultnodecolor=#rrggbb, --defaultnodecolour=#rrggbb
--defaultnodetextcolor=#rrggbb, --defaultnodetextcolour=#rrggbb
--errornodecolor=#rrggbb, --errornodecolour=#rrggbb
--mincolor=#rrggbb, --mincolour=#rrggbb
--middlecolor=#rrggbb, --middlecolour=#rrggbb
--maxcolor=#rrggbb, --maxcolour=#rrggbb

← Older revision		Revision as of 14:17, 19 February 2018
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		+	[[Category:SanXoT software package]]

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-Sanson v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the similarity graph of a set of categories.
+Sanson v1.11 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the similarity graph of a set of categories.
 A similarity graph is a graph that shows the relationship between a set of categories by taking into account how many proteins they share. This is measured with a variable f such that for categories c1 and c2, we get:
@@ Line 85: / Line 85: @@
                         The outStats file from a SanXoT integration.
     --nonparetoopacity=float
                         To "downlight" nodes not part of the Pareto front.
@@ Line 95: / Line 105: @@
     --defaultnodetextcolor=#rrggbb, --defaultnodetextcolour=#rrggbb
     --errornodecolor=#rrggbb, --errornodecolour=#rrggbb
     --mincolor=#rrggbb, --mincolour=#rrggbb
     --maxcolor=#rrggbb, --maxcolour=#rrggbb