clmorder(1) [debian man page]

clm order(1)							  USER COMMANDS 						      clm order(1)

  NAME
      clm order - reorder clusterings conformal to inclusion structure

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

  SYNOPSIS
      clm order [-prefix <string> (file multiplex prefix)] [-o <fname> (concatenated output in single file)] <cluster|stack>+

  DESCRIPTION
      Given a set of input clusterings clm order first transform it into a stack of strictly nesting clusterings. It does this by splitting  clus-
      ters  where  necessary.  It then reorders the coarsest (i.e. level-one) clustering, from large to small clusters. After that it reorders the
      second coarsest clustering conformally such that the first batch among its reordered clusters covers the level-one largest cluster, the sec-
      ond batch covers the level-one second largest cluster, and so on. Within these constraints, each batch of second-level clusters (correspond-
      ing to a single first-level cluster) is again ordered from larger to smaller clusters. This process is applied  recursively  throughout  the
      entire stack of input clusters.

      The input can be specified in multiple files, and a single file may contain multiple clusterings. The output is by default written as a con-
      catenation of matrix files, the so-called stack format. Use the -o option to specify the output file. The stacked format can be converted to
      Newick format using mcxdump(1). The output can be written to multiple files, one for each projected clustering, by using the -prefix option.
      By example, -prefix P leads to output in files named P1, P2, ..PN, where N is the number of clusters in the input,  P1  is  the  most  fine-
      grained ordered clustering, and PN is the coarsest clustering.

  OPTIONS
      -prefix (<string>)
      -o (<fname>)
	As decribed above.

  AUTHOR
      Stijn van Dongen.

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

  clm order 12-068						      8 Mar 2012							clm order(1)

clm close(1)							  USER COMMANDS 						      clm close(1)

  NAME
      clm close - Fetch connected components from graphs or subgraphs

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

  SYNOPSIS
      clm close -imx <fname> [options]

      clm close -imx fname (specify matrix input) -abc fname (specify label input) -dom fname (input domain/cluster file) [-o fname (output file)]
      [--is-undirected	(trust	input  graph  to  be  undirected)] [--write-count (output component count)] [--write-sizes (output component sizes
      (default))] [--write-cc (output components as clustering)] [--write-block (output graph restricted to -dom argument)] [--write-blockc  (out-
      put  graph  complement  of  -dom	argument)]  [-cc-bound	num  (select components with size at least num)] [-tf spec (apply tf-spec to input
      matrix)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      Use clm close to fetch the connected components from a graph. Different output modes are supported (see below). In matrix mode  (i.e.  using
      the  -imx option) the output returned with --write-cc can be used in conjunction with mcxsubs to retrieve individual subgraphs corresponding
      to connected components.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input that is in mcl native matrix format.

      -o fname (output file)
	Specify the file where output is sent to. The default is STDOUT.

      -dom fname (input domain/cluster file)
	If this option is used, clm close will, as a first step, for each of the domains in file fname retrieve the associated subgraph  from  the
	input graph. These are then further decomposed into connected components, and the program will process these in the normal manner.

      --write-count (output component count)
      --write-sizes (output component sizes (default))
      --write-cc (output components as clustering)
      --write-block (output graph restricted to -dom argument)
      --write-blockc (output graph complement of -dom argument)
	The  default  behaviour  is  currently to output the sizes of the connected components. It is also possible to simply output the number of
	components with --write-count or to write the components as a clustering in mcl format with -write-cc. Even more options exist: it is pos-
	sible to output the restriction of the input graph to a domain, or to output the complement of this restriction.

      --is-undirected (omit graph undirected check)
	With  this option the transformation to make sure that the input is undirected is omitted. This will be slightly faster. Using this option
	while the input is directed may lead to erronenous results.

      -cc-bound num (select components with size at least num)
	Transform the input matrix values according to the syntax described in mcxio(5).

  AUTHOR
      Stijn van Dongen.

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

  clm close 12-068						      8 Mar 2012							clm close(1)