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,
      duplications 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
      identical, 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
      intersection 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.

      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
        subset 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                       clm mate(1)
