clm optics(1)                   USER COMMANDS                    clm optics(1)



  NAME
      clm optics - implementation of the OPTICS reachability ordering

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

  SYNOPSIS
      clm optics -imx <fname> [options]

      clm optics -imx fname (input graph file name) -max-eps <num> (maximum
      distance considered) -min-eps <num> (minimum similarity considered)
      -min-pts <int> (minimum eps-neighbourhood size) [-icl fname (input
      clustering name)] [-o fname (output name)] [-ps fname (PostScript output
      name)] [-psx fname (scaling factor x axis)] [-psy fname (scaling factor
      y axis)] [-ps-rows <num> (split reachability plot into <num> rows)]
      [--ps-labels (show identifiers in PS output)] [-h (print synopsis,
      exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      This programs computes the reachability ordering according to the OPTICS
      clustering method. It can additionally output a PostScript plot of the
      reachability landscape. This plot can be annotated with a user-supplied
      clustering.  The program does not implement the clustering method that
      is associated with OPTICS. It is part of mcl-edge primarily as a
      visualisation aid.

  OPTIONS
      -imx fname (input file)
        The input file, encoding a graph in native format.

      -max-eps <num> (maximum distance considered)
      -min-eps <num> (minimum similarity considered)
      -min-pts <int> (minimum eps-neighbourhood size)
        These encode the OPTICS parameters. Use -max-eps if the edge weights
        encode a distance (for example the Euclidean distance between points),
        use -min-eps if the edge weights encode a similarity.

      -o fname (output file name)
      -ps fname (PostScript file name)
      -icl fname (input clustering name)
        The -o fname option controls the name of the file in which the
        reachability values are written. By default these values are written
        to STDOUT.

        If -ps fname is supplied the program will additionally output a
        visualisation of the reachability landscape plot in a PostScript file.

        It is possible, in addition to -ps, to specify a clustering with
        -icl fname.  Each vertical bar in the landscape plot will be coloured
        according to cluster membership, that is, nodes in the same cluster
        will have the same colour. This can be a useful way to visualise
        separation properties of clusterings.

      -psx fname (scaling factor x axis)
      -psy fname (scaling factor y axis)
      --ps-labels (show identifiers in PS output)
      -ps-rows <num> (split reachability plot into <num> rows)
        By default the PostScript output will be scaled to fit onto an A3
        page.  The scaling options -psx and -psy can be used as additional
        scaling factors. By default these are set 1.0.

        The --ps-labels can be used to annotate each vertical bar in the
        landscape plot with the mcl-edge identifier of the corresponding node.

        The -ps-rows option sets the number of rows. This is the primary
        option affect the width of a bar.

  AUTHOR
      Stijn van Dongen.

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



  clm optics 14-137                 16 May 2014                    clm optics(1)
