clmimac(1) [debian man page]

clm imac(1)							  USER COMMANDS 						       clm imac(1)

  NAME
      clm imac - Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

      clmimac  is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode imac.
      The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.

  SYNOPSIS
      clm imac -imx <fname> [options]

      clm imac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output  DAG)]  [-overlap	str  (overlap  mode)]  [-sort  str
      (size|revsize|lex|none)]	[-strict  num (in 0..1)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      Use clm imac to interpret matrices (as clusterings) output by mcl using mcl's -dump ite option.

      Use clm imac only if you have a special reason; the normal usage of mcl is to do multiple runs for varying -I parameters and use	the  clus-
      terings output by mcl itself.  One reason is if you are interested in clusterings with overlap; early MCL iterands generally induce cluster-
      ings possessing overlap.	Another reason is to investigate how the cluster structure associated with the MCL process evolves over time.

  OPTIONS
      -imx fname (input file)
	The input file is presumably an MCL iterand resulting from the mcl option -dump ite.

      -strict num (in 0..1)
	Higher values (up until 1) will thin out the DAG constructed by clm imac. The default value is 0.00001, yielding the full DAG.

      -o fname (file name/stem)
	Write to file named fname.

      -dag fname (output DAG)
	Write the DAG (directed acyclic graph) constructed from the input to file. This DAG is constructed according to the  structure	associated
	with  diagonally positive semi-definite matrices as described in the PhD thesis Graph clustering by flow simulation.  Consult mclfamily(7)
	for references.

      -sort str (size|revsize|lex|none)
	Sort the clusters either by increasing size, decreasing size, lexicographically by the indices they contain, or use the clustering exactly
	as obtained from the interpretation routine.

      -overlap mode (overlap mode)
	With  mode  set  to  cut,  remove  any overlap by allocating the nodes in overlap to the first cluster in which they were found. Mode keep
	leaves overlap unchanged, and mode split results in overlapping parts excised and introduced as clusters in their own right.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  clm imac 12-068						      8 Mar 2012							 clm imac(1)

clm close(1)							  USER COMMANDS 						      clm close(1)

  NAME
      clm close - Fetch connected components from graphs or subgraphs

      clmclose	is  not  in  actual  fact  a program. This manual page documents the behaviour and options of the clm program when invoked in mode
      close. The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.

  SYNOPSIS
      clm close -imx <fname> [options]

      clm close -imx fname (specify matrix input) -abc fname (specify label input) -dom fname (input domain/cluster file) [-o fname (output file)]
      [--is-undirected	(trust	input  graph  to  be  undirected)] [--write-count (output component count)] [--write-sizes (output component sizes
      (default))] [--write-cc (output components as clustering)] [--write-block (output graph restricted to -dom argument)] [--write-blockc  (out-
      put  graph  complement  of  -dom	argument)]  [-cc-bound	num  (select components with size at least num)] [-tf spec (apply tf-spec to input
      matrix)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      Use clm close to fetch the connected components from a graph. Different output modes are supported (see below). In matrix mode  (i.e.  using
      the  -imx option) the output returned with --write-cc can be used in conjunction with mcxsubs to retrieve individual subgraphs corresponding
      to connected components.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input that is in mcl native matrix format.

      -o fname (output file)
	Specify the file where output is sent to. The default is STDOUT.

      -dom fname (input domain/cluster file)
	If this option is used, clm close will, as a first step, for each of the domains in file fname retrieve the associated subgraph  from  the
	input graph. These are then further decomposed into connected components, and the program will process these in the normal manner.

      --write-count (output component count)
      --write-sizes (output component sizes (default))
      --write-cc (output components as clustering)
      --write-block (output graph restricted to -dom argument)
      --write-blockc (output graph complement of -dom argument)
	The  default  behaviour  is  currently to output the sizes of the connected components. It is also possible to simply output the number of
	components with --write-count or to write the components as a clustering in mcl format with -write-cc. Even more options exist: it is pos-
	sible to output the restriction of the input graph to a domain, or to output the complement of this restriction.

      --is-undirected (omit graph undirected check)
	With  this option the transformation to make sure that the input is undirected is omitted. This will be slightly faster. Using this option
	while the input is directed may lead to erronenous results.

      -cc-bound num (select components with size at least num)
	Transform the input matrix values according to the syntax described in mcxio(5).

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  clm close 12-068						      8 Mar 2012							clm close(1)