.\" Copyright (c) 2022 Stijn van Dongen
.TH "clm imac" 1 "9 Oct 2022" "clm imac 22-282" "USER COMMANDS "
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.SH NAME
clm_imac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) 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 \fIimac\fP\&. The options \fB-h\fP, \fB--apropos\fP,
\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
in all \fBclm\fP modes\&. They are described
in the \fBclm\fP manual page\&.
.SH SYNOPSIS

\fBclm imac\fP -imx <fname> [options]

\fBclm imac\fP
\fB-imx\fP fname (\fIinput file\fP)
\fB[-o\fP fname (\fIname/stem for output\fP)\fB]\fP
\fB[-dag\fP fname (\fIoutput DAG\fP)\fB]\fP
\fB[-overlap\fP str (\fIoverlap mode\fP)\fB]\fP
\fB[-sort\fP str (\fIsize|revsize|lex|none\fP)\fB]\fP
\fB[-strict\fP num (\fIin 0\&.\&.1\fP)\fB]\fP
\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
.SH DESCRIPTION

Use \fBclm imac\fP to interpret matrices (as clusterings) output by \fBmcl\fP using
\fBmcl\fP\&'s \fB-dump\fP\ \&\fBite\fP option\&.

Use \fBclm imac\fP only if you have a special reason; the normal usage
of \fBmcl\fP is to do multiple runs for varying \fB-I\fP parameters
and use the clusterings output by \fBmcl\fP 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\&.
.SH OPTIONS

.ZI 2m "\fB-imx\fP fname (\fIinput file\fP)"
\&
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The input file is presumably an MCL iterand resulting
from the mcl option \fB-dump\fP\ \&\fBite\fP\&.
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.ZI 2m "\fB-strict\fP num (\fIin 0\&.\&.1\fP)"
\&
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Higher values (up until 1) will thin out the DAG
constructed by \fBclm imac\fP\&. The default value is 0\&.00001,
yielding the full DAG\&.
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.ZI 2m "\fB-o\fP fname (\fIfile name/stem\fP)"
\&
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Write to file named \fIfname\fP\&.
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.ZI 2m "\fB-dag\fP fname (\fIoutput DAG\fP)"
\&
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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 \fIGraph clustering by flow simulation\fP\&.
Consult \fBmclfamily(7)\fP for references\&.
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.ZI 2m "\fB-sort\fP str (\fIsize|revsize|lex|none\fP)"
\&
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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\&.
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.ZI 2m "\fB-overlap\fP mode (\fIoverlap mode\fP)"
\&
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With \fImode\fP set to \fIcut\fP, remove any overlap by allocating the
nodes in overlap to the first cluster in which they were found\&. Mode
\fIkeep\fP leaves overlap unchanged, and mode \fIsplit\fP results in overlapping
parts excised and introduced as clusters in their own right\&.
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.SH AUTHOR

Stijn van Dongen\&.
.SH SEE ALSO

\fBmclfamily(7)\fP for an overview of all the documentation
and the utilities in the mcl family\&.