clmformat(1)                    USER COMMANDS                     clmformat(1)



  NAME
      clm format - display cluster results in readable form

      (optionally with labels and/or cohesion and stickiness measures
      attached).

      Unless used with the -dump fname or --dump option, clm format depends on
      the presence of the macro processor zoem, as described further below.

      The -icl fname input clustering option is always required. The
      -imx fname input matrix option is required in fancy mode. The tab file
      option -tab fname is needed if you want label information in the output
      rather than mcl identifiers.

  SYNOPSIS
      clm format has two different modes of output: dump and fancy.  If
      neither is specified, fancy is used. In this mode, clm format generates
      a large arrary of performance measures related to nodes and clusters in
      both interlinked html output and plain text files. The files will be
      contained in an output directory that is newly created if not yet
      existing. In fancy mode the -imx option is required and the macro
      processor zoem must be available (http://micans.org/zoem).

      If dump is specified (see below how to do this) clm format just
      generates a dump file where each line contains a cluster in the form of
      tab-separated indices, or tab-separated labels in case the -tab option
      is used. This dump is easy to parse with a simple or even quick-and-
      dirty script.  You can include some very simple performance measures in
      this dump file by supplying --dump-measures. Use -dump fname to specify
      the name of the file to dump to, rather than having clm format construct
      a file name by itself.

      clm format can combine the both modes by using either --dump or
      -dump fname and --fancy. In this case the dump file will be created in
      the output directory that is used by fancy mode.

      clm format

      -icl fname (input cluster file) -imx fname (input matrix/graph file)
      [-tf spec (apply tf-spec to input matrix)] [-pi num (apply pre-inflation
      to matrix)] [-tab fname (read tab file)] [--lazy-tab (allow mismatched
      tab-file)] [-lump-count n (node threshold)] [--dump (write dump to
      dump.<icl-name>)] [-dump fname (write dump to file)] [--dump-pairs
      (write cluster/node pair per line)] [--dump-measures (write simple
      performance measures)] [-dump-node-sep str (separate entries with str)]
      [--fancy (spawn information blizzard)] [-dir dirname (write results to
      directory)] [-infix str (use after base name/directory)] [-nsm fname
      (output node stickiness file)] [-ccm fname (output cluster cohesion
      file)] [--adapt (allow domain mismatch)] [--subgraph (take subgraph with
      --adapt)] [-zmm fname (assume macro definitions are in fname)] [-fmt
      fname (write to encoding file fname)] [-h (print synopsis, exit)]
      [--apropos (print synopsis, exit)] [--version (print version, exit)]

      Consult the option descriptions and the introduction above for
      interdependencies of options.

      clm format generates in fancy mode a logical description of the to-be-
      formatted content in a very small vocabulary of format-specific zoem
      macros. The appearance of the output can be easily changed by adapting a
      zoem macro definition file (also output by clm format) that is used by
      the zoem interpreter to interpret the logical elements.

      The output format is apt to change over subsequent releases, as a result
      of user feedback. Such changes will most likely be confined to the zoem
      macro definition file.

      The OUTPUT EXPLAINED section further below is likely to be of interest.

  DESCRIPTION
      The primary function of clm format is to display cluster results and
      associated confidence measures in a readable form, by listing clusters
      in terms of the labels associated with the indices that are used in the
      mcl matrix. The labels must be stored in a so called tab file; see the
      -tab option for more information.

      NOTE
      clm format output is in the form of zoem macros.  You need to have zoem
      installed in your system if you want clm format to be of use. Zoem will
      not be necessary if you are using the -dump option.

      The -imx mx option is required unless the -dump option is used. The
      latter option results in special behaviour described under the
      -dump fname entry.

      Output is by default written in a directory that is newly created if it
      does not yet exist (normally several files will be created, for which
      the directory acts as a natural container).  It is possible to simply
      output to the current directory, for that you need to specify -dir ./.
      If -dir is not specified, the output directory fmt.<clname> will be
      used, where <clname> is the argument to the -cl option. In the output
      directory, clm format will normally write two files. One contains zoem
      macros encoding formatted output (the encoding file), and the second
      (the definition file) contains zoem macro definitions which are used by
      the former.

      The encoding file is by default called fmt.azm (cf. the -fmt fname
      option).  It contains zoem macros. It imports the macro definition file
      called clmformat.zmm that is normally also written by clm format.
      Another macro definition file can be specified by using the
      -zmm <defsname> option. In this case clm format will refrain from
      writing the definition file and replace mentions of clmformat.zmm in the
      encoding file by <defsname>.

      The encoding file needs to be processed by issuing one of the following
      commands from within the directory where the file is located.

         zoem -i fmt -d html
         zoem -i fmt -d txt

      The first will result in HTML formatted output, the second in plain text
      format. Obviously, you need to have installed zoem (e.g. from
      http://micans.org/zoem/src/) for this to work.

      For each cluster a paragraph is output. First comes a listing of other
      clusters (in order of relevance, possibly empty) for which a significant
      amount of edges exists between the other and the current cluster. Second
      comes a listing of the nodes in the current cluster. For each node a
      small sublist is made (in order of relevance, possibly empty) of other
      clusters in which the node has neighbours and for which the total sum of
      corresponding edge weights is significant.  Several quantities are
      output for each node/cluster pair that is deemed relevant. These are
      explained in the section OUTPUT EXPLAINED.

      Clusters will by default be output to file until the total node count
      has exceeded a threshold (refer to the -lump-count option).

      clm format also shows how well each node fits in the cluster it is in
      and how cohesive each cluster is, using simple but effective measures
      (described in section OUTPUT EXPLAINED).  This enables you to compare
      the quality of the clusters in a clustering relative to each other, and
      may help in identifying both interesting areas and areas for which
      cluster structure is hard to find or perhaps absent.

  OPTIONS
      -icl fname (input cluster file)
        Name of the clustering file.

      -imx fname (input matrix/graph file)
        Name of the graph/matrix file.

      -tf spec (apply tf-spec to input matrix)
        Transform the input matrix values according to the syntax described in
        mcxio(5).

      -tab fname (read tab file)
        The file fname should be in tab format. Refer to mcxio(5).

      --lazy-tab (allow mismatched tab-file)
        Allow missing and spurious entries in the tab file.

      -dump fname (write dump to file)
        Clusters are written to file. For each cluster a single line is
        written containing all indices of all nodes in that cluster. The
        indices are separated by tabs. If a tab file is specified, the indices
        are replaced by the corresponding tab file entry.

      --dump (write dump to file)
        As -dump fname except that clm format writes to the file named
        dump.<icl-name> where <icl-name> is the argument to the -icl option.

      -infix str (incorporate in base name)
        str is included in the output file names.  This can be used to store
        the results of different clm format runs (e.g. with differing -tf
        arguments) in the same directory.

      --fancy (force fancy mode)
        This enforces fancy mode if either of -dump or --dump is given. The
        dump file will be created in the output directory.

      --dump-pairs (write cluster/node pair per line)
        Rather than writing a single cluster on each line, write a single
        cluster index/node (either tab entry or index) pair per line.  Works
        in conjunction with the -tab and -imx options.

      --dump-measures (write simple performance measures)
        If an input matrix is specified with -imx fname, three measures of
        efficiency are prepended, respectively the simple projection score,
        efficiency or coverage, and the max-efficiency or max-coverage.

      -dump-node-sep str (separate entries with str)
        Separate entries in the dump file with str.

      -pi num (apply pre-inflation to matrix)
        Apply pre-inflation to the matrix specified with the -imx option.
        This will cause the efficiency scores to place a higher reward on
        high-weight edges being covered by a clustering (assuming that num is
        larger than one).

        This option is also useful when mcl itself was instructed to use pre-
        inflation when clustering a graph.

      -lump-count n (node threshold)
        The zoem file is created such that during zoem processing clusters are
        formatted and output within a single file until the node threshold has
        been exceeded. A new file is then opened and the procedure repeats
        itself.

      --adapt (allow domain mismatch)
        Allow the cluster domain to differ from the graph domain. Presumably
        the clustering is a clustering of a subgraph. The cohesion and
        stickiness measures will pertain to the relevant part of the graph
        only.

      --subgraph (use restriction)
        If the cluster domain is a subset of the graph domain, the cohesion
        and stickiness measures will by default still pertain to the entire
        graph. By setting this option, the measures will pertain to the
        subgraph induced by the cluster domain.

      -dir dirname (write results to directory)
        Use dirname as output directory. It will be created if it does not
        exist already.

      -fmt fname (write to encoding file fname)
        Write to encoding file fname rather than the default fmt.azm.  It is
        best to supply fname with the standard zoem suffix .azm. Zoem will
        process file of any name, but those lacking the .azm suffix must be
        specified using the zoem -I fname option.

      -zmm defsname (assume macro definitions are in fname)
        If this option is used, clm format will not output the definition
        file, and mentions of the definition file in the encoding file will
        use the file name defsname. This option assumes that a valid
        definition file by the name of defsname does exist.

      -nsm fname (output node stickiness file)
        This option specifies the name in which to store (optionally) the node
        stickiness matrix. It has the following structure. The columns range
        over all elements in the graph as specified by the -imx option.  The
        rows range over the clusters as specified by the -icl option.  The
        entries contain the projection value of that particular node onto that
        particular clusters, i.e. the sum of the weights of all arcs going out
        from the node to some node in that cluster, written as a fraction
        relative to the sum of weights of all outgoing arcs.

      -ccm fname (output cluster cohesion file)
        This option specifies the name of the file in which to store
        (optionally) the cluster cohesion matrix. It has the following
        structure.  Both columns and rows range over all clusters in the
        clustering as specified by the -icl option. An entry specifies the
        projection of one cluster onto another cluster, which is simply the
        average of the projection value onto the second cluster of all nodes
        in the first cluster.

  OUTPUT EXPLAINED
      What follows is an explanation of the output provided by the standard
      zoem macros. The output comes in a pretty terse number-packed format.
      The decision was made not to include headers and captions in the output
      in order to keep it readable.  You might want to print out the following
      annotated examples.  At the same side of the equation, the following is
      probably tough reading unless you have an actual example of clmformatted
      output at hand.

      If you are reading this in a terminal, you might need to resize it to
      have width larger than 80 columns, as the examples below are formatted
      in verbatim mode.

      Below mention is made of the projection value for a node/cluster pair.
      This is simply the total amount of edge weights for that node in that
      cluster (corresponding to neighbours of the node in the cluster)
      relative to the overall amount of edge weights for that node
      (corresponding to all its neighbours).  The coverage measure (refered to
      as cov) is also used. This is similar to the projection value, except
      that a) the coverage measure rewards the inclusion of large edge weights
      (and penalizes the inclusion of insignificant edge weights) and b)
      rewards node/cluster pairs for which the neighbour set of the node is
      very similar to the cluster.  The maximum coverage measure (refered to
      as maxcov) is similar to the normal coverage measure except that it
      rewards inclusion of large edge weights even more.  The cov and maxcov
      performance measures have several nice continuity and monotonicity
      properties and are described in [1].

      Example cluster header

      Cluster 0 sz 15 self 0.82 cov 0.43-0.26
         10: 0.11
         18: 0.05
         12: 0.02

      explanation

      Cluster 0 sz 15 self 0.82 cov 0.43-0.26
              |    |       |           | |
              clid count   proj      cov covmax

         10: 0.11
          |  |
      clidx1 projx1

         18: 0.05
          |  |
      clidx2 projx2

      clid    Numeric cluster identifier (arbitrarily) assigned by MCL.
      count   The size of cluster clid.
      proj    Projection value for cluster clid [d].
      cov     Coverage measure for cluster clid [d].
      maxcov  Max-coverage measure for cluster clid [d].
      clidx1  Index of other cluster sharing relatively many edges.
      projx1  Projection value for the clid/clidx1 pair of clusters [e].
      clidx2  :
      projx2  : as clidx1 and projx1

      Example inner node
      An inner node is listed under a cluster, and it is simply a member of
      that cluster. The name is as opposed to 'outer node', described below.

      [foo bar zut]
          21     7-5      0.73 0.420-0.331  0.282-0.047  0.071-0.035 <3.54>
            10   6/3      0.16 0.071-0.047  0.268-0.442
            12   4/2      0.11 0.071-0.035  0.296-0.515

      explanation

      [label]
          21     7-5      0.73 0.420-0.331  0.282-0.047  0.071-0.035 <3.54>
           |     | |      |        | |          | |          | |     |
          idx  nbi nbo    proj   cov covmax max_i min_i  max_o-min_o SUM

            10   6/3      0.16 0.268-0.442  0.071-0.047
             |   | |      |        | |          | |
        clusid  sz nb     proj   cov covmax max_i min_i

      label   Optional; with -tab <tabfile> option.
      idx     Numeric (mcl) identifier.
      nbi     Count of the neighbours of node idx within its cluster.
      nbo     Count of the neighbours of node idx outside its cluster.
      proj    Projection value [a] of nbi edges.
      cov     Skewed projection [b], rewards inclusion of large edge weights.
      covmax  As cov above, rewarding large edge weights even more.
      max_i   Largest edge weight in the nbi set, normalized [c].
      min_i   Smallest edge weight in the nbi set [c].
      max_o   Largest edge weight outside the nbi set [c]
      min_o   Smallest edge weight outside the nbi set [c].
      SUM     The sum of all edges leaving node idx.

      clusid  Index of other cluster that is relevant for node idx.
      sz      Size of that cluster.
      nb      Count of neighbours of node idx in cluster clusid.
      proj    Projection value of edges from node idx to cluster clusid.
      cov     Skewed projection of edges from node idx to cluster clusid.
      covmax  Maximally skewed projection, as above.
      max_o   Largest edge weight for node idx to cluster clusid [c].
      min_o   Smallest edge weight for  node idx to cluster clusid [c].

      Example outer node
      An outer node is listed under a cluster. The node is not part of that
      cluster, but seems to have substantial connections to that cluster.

      [zoo eek few]
          29   18#2        2-5      0.65 0.883-0.815  0.436-0.218  0.073-0.055
                            /4      0.27 0.070-0.109  0.073-0.055

      explanation

      [label]
          29   18#2        2-5      0.65 0.883-0.815  0.436-0.218  0.073-0.055
          |    |  |        | |      |        | |          | |          | |
          idx  cl sz     nbi nbo    proj   cov maxcov max_i min_i  max_o min_o
               id
                            /4      0.27 0.070-0.109  0.073-0.055  <2.29>
                             |      |        | |          | |      |
                             nb     proj   cov maxcov max_i min_i  SUM

      label   Optional; with -tab <tabfile> option.
      idx     Numeric (mcl) identifier
      clid    Index of the cluster that node idx belongs to
      sz      Size of the cluster that node idx belongs to
      proj    :
      cov     :  All these entries are the same as described above
      covmax  :  for inner nodes, pertaining to cluster clid,
      max_i   :  i.e. the native cluster for node idx
      min_i   :  (it is a member of that cluster).
      max_o   :
      min_o   :

      nb      The count of neighbours of node idx in the current cluster
      proj    Projection value for node idx relative to current cluster.
      cov     Skewed projection (rewards large edge weights), as above.
      covmax  Maximally skewed projection, as above.
      max_o   Largest edge weight for node idx in current cluster [c].
      min_o   smallest edge weight for node idx in current cluster [c].
      SUM     The sum of *all* edges leaving node idx.

    [a]  The projection value for a node relative to some subset of its
         neighbours is the sum of edge weights of all edges to that subset.
         The sum is witten as a fraction relative to the sum of edge weights
         of all neighbours.

    [b]  cov and covmax stand for coverage and maximal coverage.  The coverage
         measure of a node/cluster pair is a generalized and skewed projection
         value [a] that rewards the presence of large edge weights in the
         cluster, relative to the collection of weights of all edges departing
         from the node. The maxcov measure is a projection value skewed even
         further, correspondingly rewarding the inclusion of large edge
         weights. The cov and maxcov performance measures have several nice
         continuity properties and are described in [1].

    [c]  All edge weights are written as the fraction of the sum SUM of all
         edge weights of edges leaving node idx.

    [d]  For clusters the projection value and the coverage measures are
         simply the averages of all projection values [a], respectively
         coverage measures [b], taken over all nodes in the cluster.  The
         cluster projection value simply measures the sum of edge weights
         internal to the cluster, relative to the total sum of edge weights of
         all edges where at least one node in the edge is part of the cluster.

    [e]  The projection value for start cluster x and end cluster y is the sum
         of edge weights of edges between x and y as a fraction of the sum of
         all edge weights of edges leaving x.

  AUTHOR
      Stijn van Dongen.

  REFERENCES
      [1] Stijn van Dongen. Performance criteria for graph clustering and
      Markov cluster experiments. Technical Report INS-R0012, National
      Research Institute for Mathematics and Computer Science in the
      Netherlands, Amsterdam, May 2000.
      http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z

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



  clmformat 1.008, 09-308           4 Nov 2009                      clmformat(1)
