Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:44Z

Mtrevisan at 14:24, 3 October 2017

2017-10-03T14:24:40Z

Mtrevisan: Created page with "Arbor v1.05 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the tree graph of a s..."

2017-10-03T14:24:12Z

Created page with "Arbor v1.05 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the tree graph of a s..."

New page

Arbor v1.05 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the tree graph of a set of categories, showing the position of a given list of categories in the tree, along with category information.

Arbor needs four input files:

:* a stats file, the outStats file from SanXoT (using the -z command); if this is omitted, then the tree will only distinguish the categories in the list from the other categories above them (not showing the values of the protein within the category).
:* a higher level list to graph (using the -c command)
:* a relations file (using -r command)
:* a list of links between higher level elements, such as the table_allPaths.xls from GOconnect (using the -b command)

And delivers three output files:

:* the graph in PNG format (default suffix: "_outTree.png")
:* the DOT language text file used to generate the graph (default suffix: "_outTree.gv")
:* a log file (default suffix: "_logFile")

Usage:
arbor.py -z[stats file] -r[relations file] -c[higher level list file] -b[links 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, --biglist A list of links between higher level elements, such as
the table_allPaths.xls from GOconnect. It must be a tab
separated values text file, containing any identifier
in the first column (this column will not be imported,
but originally it was intended to contain protein
identifiers for each path), containing in each row (from
the second column on) a possible path from top to the
most specific element.
-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.
-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.
-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.
-z, --outstats=filename
The outStats file from a SanXoT integration (optional,
see above).

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Arbor - Revision history

Mtrevisan at 14:17, 19 February 2018

Mtrevisan at 14:24, 3 October 2017

Mtrevisan: Created page with "Arbor v1.05 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate the tree graph of a s..."