


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


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

      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|rev-
      size|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 clusterings
      output  by  mcl itself.  One reason is if you are interested in cluster-
      ings with overlap; early MCL iterands generally induce clusterings  pos-
      sessing  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,  lexico-
        graphically 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



  clm imac 1.008, 09-308      4 Nov 2009                          1





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


        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.















































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