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.  These three options are described in the clmprotocols
        manual page.  The following set of options, if given to as many
        commands, defines three jobs, each running four threads.

        -t 4 -J 3 -j 0 -o out.0
        -t 4 -J 3 -j 1 -o out.1
        -t 4 -J 3 -j 2 -o out.2

        The output can then be collected with

        mcx collect --add-column -o out.all out.[0-2]


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



  mcx clcf 14-137                   16 May 2014                      mcx clcf(1)
