clmimac(1)

NAME
clmimac - Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

SYNOPSIS
clmimac -imx <fname> [options] clmimac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output DAG)] [-t num (tightness parameter)] [-tstep num (tightness step increment)] [-tbound num (tightness ceiling)] [--enstrict (remove overlap)] [--center (use center in defining tightness)] [-sort str (size|revsize|lex|none)] [-h (list help)] [--apropos (list synopsis of all options)]

DESCRIPTION
Use clmimac to interpret matrices (as clusterings) output by mcl using mcl's -dump ite option. Use clmimac only if you have a special reason; the normal usage of mcl is to do multiple runs for varying -I parameters and use the clusterings output by mcl itself. One reason is if you are interested in clusterings with overlap; early MCL iterands generally induce clusterings possessing overlap. Another reason is to investigate how the cluster structure associated with the MCL process evolves over time.

OPTIONS
The input file is presumably an MCL iterand resulting from the mcl option -dump ite.
num should be a number in the range [0.0, 100.0]. The highter num, the less overlap will result. Its default value is 0. Multiple tightness parameters can be specified by using the -tstep option.
Repeat interpretation for tightness parameters that increaes with stepsize num, starting with the value given by the -t option. By default, interpretation is not repeated.
Ceiling for the tightness parameter as resulting from the -t and -tstep options.
This option will generally result in more stringent clusterings (containing fewer overlap), and tries to retain the most significant entries. Use this option only on matrices resulting from the MCL -dump dag option, and do not use it on matrices resulting from the -dump ite option.
Write to file named fname. In case multiple tightness parameters are specified, use fname as stem for the output file names.
Write the DAG (directed acyclic graph) constructed from the input to file. This DAG is constructed according to the structure associated with diagonally positive semi-definite matrices as described in the PhD thesis Graph clustering by flow simulation. Consult mclfaq(7) for references.
Sort the clusters either by increasing size, decreasing size, lexicographically by the indices they contain, or use the clustering exactly as obtained from the interpretation routine.
Remove overlap should it be found, by allocating the nodes in overlap to the first cluster in which they were found.
Print help, this could possibly be the same output as supplied with --apropos.
List a one-line synopsis for all options.

AUTHOR
Stijn van Dongen.

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