clm imac - Interpret Matrices (c.q. MCL iterands output by
mcl) As
Clusterings.
clmimac is not in actual fact a program. This manual page documents the
behaviour and options of the clm program when invoked in mode
imac. The
options
-h,
--apropos,
--version,
-set,
--nop are accessible in all
clm modes. They are described in the
clm manual page.
clm imac -imx <fname> [options]
clm imac -imx fname (
input file)
[-o fname
(
name/stem for output)
] [-dag fname (
output
DAG)
] [-overlap str (
overlap mode)
]
[-sort str (
size|revsize|lex|none)
] [-strict num
(
in 0..1)
] [-h (
print synopsis, exit)
]
[--apropos (
print synopsis, exit)
] [--version
(
print version, exit)
]
Use
clm imac to interpret matrices (as clusterings) output by
mcl
using
mcl's
-dump ite option.
Use
clm imac 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.
-imx fname (
input file)
The input file is presumably an MCL iterand resulting from the mcl option
-dump ite.
-strict num (
in 0..1)
Higher values (up until 1) will thin out the DAG constructed by
clm imac.
The default value is 0.00001, yielding the full DAG.
-o fname (
file name/stem)
Write to file named
fname.
-dag fname (
output DAG)
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
mclfamily(7) for references.
-sort str (
size|revsize|lex|none)
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.
-overlap mode (
overlap mode)
With
mode set to
cut, remove any overlap by allocating the nodes
in overlap to the first cluster in which they were found. Mode
keep
leaves overlap unchanged, and mode
split results in overlapping parts
excised and introduced as clusters in their own right.
Stijn van Dongen.
mclfamily(7) for an overview of all the documentation and the utilities
in the mcl family.