


  clm mate(1)               USER COMMANDS               clm mate(1)


  NAME
      clm mate - compute best matches between two clusterings

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

  SYNOPSIS
      clm mate [-o fname (output file name)] [-b  (omit  headers)]  [--one-to-
      many  (require  multiple hits in <clfile1>)] [-h (print synopsis, exit)]
      [--apropos (print synopsis, exit)]  [--version  (print  version,  exit)]
      <clfile1> <clfile2>

  DESCRIPTION
      clm  mate  computes  for  each  cluster  X  in clfile1 all clusters Y in
      clfile2 that have non-empty intersection and outputs  a  line  with  the
      data points listed below.

         overlap(X,Y)               # 2 * size(meet(X,Y)) / (size(X)+size(Y))
         index(X)                   # name of cluster
         index(Y)                   # name of cluster
         size(meet(X,Y))
         size(X-Y)                  # size of left difference
         size(Y-X)                  # size of right difference
         size(X)
         size(Y)
         projection(X, clfile2)     # see below
         projection(Y, clfile1)     # see below

      The  projected  size of a cluster X relative to a clustering K is simply
      the sum of all the nodes shared between any cluster Y in K and X, dupli-
      cations  allowed.  For  example, the projected size of (0,1) relative to
      {(0,2,4), (1,4,9), (1,3,5)} equals 3.

      The overlap between X and Y is exactly 1.0 if the two clusters are iden-
      tical,  and  for nearly identical clusterings the score will be close to
      1.0.

      All of this information can also be obtained from the contingency matrix
      defined for two clusterings.  The [i,j] row-column entry in a contigency
      matrix between to clusterings gives the number of entries in the  inter-
      section between cluster i and cluster j from the respective clusterings.
      The other information is implicitly present; the total number  of  nodes
      in clusters i and j for example can be obtained as the sum of entries in
      row i and column j respectively, and the difference counts can  then  be
      obtained by substracting the intersection count.  The contingency matrix
      can easily be computed using mcx; e.g.


      mcx /clfile2 lm /clfile1 lm tp mul /ting wm

      will create the contingency matrix in mcl  matrix  format  in  the  file
      ting, where columns range over the clusters in clfile1.



  clm mate 1.008, 09-308      4 Nov 2009                          1





  clm mate(1)               USER COMMANDS               clm mate(1)


      The  output  can  be  put  to good use by sorting it numerically on that
      first score field. It is advisable to use a stable sort routine (use the
      -s  option  for UNIX sort) From this information one can quickly extract
      the closest clusters between two clusterings.

  OPTIONS
      -o fname (output file name)
        Specify the name of the output file.

      -b (omit headers)
        Batch mode, omit column names.

      --one-to-many (require multiple hits in <clfile1>)
        Do not output information for clusters in the first file that are sub-
        set of a cluster in the second file.

  AUTHOR
      Stijn van Dongen.

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



































  clm mate 1.008, 09-308      4 Nov 2009                          2


