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)]
      [--write-count (output component count)] [--write-sizes (output
      component sizes (default))] [--write-cc (output components as
      clustering)] [-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)
        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.

      -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 1.008, 09-308           4 Nov 2009                      clm close(1)
