clmclose(1) [debian man page]

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)

mcx clcf(1)							  USER COMMANDS 						       mcx clcf(1)

  NAME
      mcx clcf - compute the clustering coefficient of a graph

  SYNOPSIS
      mcx clcf [options] [matrix-file]

      mcxclcf  is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode clcf.
      The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described  in  the  mcx  manual
      page.

      mcx clcf [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-tab <fname> (use tab file)] [-o <fname> (write to this
      file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are used)] [-j <intj>  (this  job  has  index  <intj>)]	[--summary
      (return mean clustering coefficient)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      mcx clcf computes the clustering coefficient of a graph.

      The  input  graph/matrix,  if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input instead by using
      the -abc option.	Refer to mcxio(5) for a description of these two input formats.  By default mcx diameter  reads  from  STDIN  and  expects
      matrix format.  To specify label input from STDIN use -abc -.

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

      -imx <fname> (input matrix)
	The file name for input. STDIN is assumed if not specified.

      -o <fname> (output file)
	The file name for output. STDOUT is the default output stream.

      -tab <fname> (use tab file)
	This  option causes the output to be printed with the labels found in the tab file.  With -abc this option will, additionally, construct a
	graph only on the labels found in the tab file.  If this option is used in conjunction with -imx the tab domain and the matrix domain  are
	required to be identical.

      --summary (return mean clustering coefficient)
	By  the  default a 1-column table (with row names included) is output, one row for each node. This option causes the output of the average
	clustering coefficient only.

      -t <int> (use <int> threads)
      -J <intJ> (a total of <intJ> jobs are used)
      -j <intj> (this job has index <intj>)
	Computing clustering coefficients is time-intensive for large graphs. If you have multiple CPUs available consider using as many  threads.
	Additionally  it  is possible to spread the computation over multiple jobs/machines. Conceptually, each job takes a number of threads from
	the total thread pool. If job control is used (the -J option is used) then the number of jobs should not exceed  the  number  of  threads.
	The  total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job. Addi-
	tionally, the number of threads specified signifies the total added amount of all threads across all machines and must be the same for all
	jobs.  This  number is used by each job to infer its own set of tasks. The following set of options, if given to as many commands, defines
	three jobs, each running four threads.

	-t 12 -G 3 -g 0
	-t 12 -G 3 -g 1
	-t 12 -G 3 -g 2

  SEE ALSO
      mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcx clcf 12-068						      8 Mar 2012							 mcx clcf(1)