Man page - clmoptics(1)
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Manual
clm_optics
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO
NAME
clm_optics - implementation of the OPTICS reachability ordering
clmoptics is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode optics . The options -h , --apropos , --version , -set , --nop are accessible in all clm modes. They are described in the clm manual page.
SYNOPSIS
clm optics -imx <fname> [options]
clm optics -imx fname ( input graph file name ) -max-eps <num> ( maximum distance considered ) -min-eps <num> ( minimum similarity considered ) -min-pts <int> ( minimum eps-neighbourhood size ) [-icl fname ( input clustering name ) ] [-o fname ( output name ) ] [-ps fname ( PostScript output name ) ] [-psx fname ( scaling factor x axis ) ] [-psy fname ( scaling factor y axis ) ] [-ps-rows <num> ( split reachability plot into <num> rows ) ] [--ps-labels ( show identifiers in PS output ) ] [-h ( print synopsis, exit ) ] [--apropos ( print synopsis, exit ) ] [--version ( print version, exit ) ]
DESCRIPTION
This programs computes the reachability ordering according to the OPTICS clustering method. It can additionally output a PostScript plot of the reachability landscape. This plot can be annotated with a user-supplied clustering. The program does not implement the clustering method that is associated with OPTICS . It is part of mcl-edge primarily as a visualisation aid.
OPTIONS
-imx
fname (
input file
)
The input file, encoding a graph in native format.
-max-eps
<num> (
maximum distance considered
)
-min-eps
<num> (
minimum similarity
considered
)
-min-pts
<int> (
minimum eps-neighbourhood
size
)
These encode the
OPTICS
parameters. Use
-max-eps
if the edge weights encode a distance (for
example the Euclidean distance between points), use
-min-eps
if the edge weights encode a similarity.
-o
fname
(
output file name
)
-ps
fname (
PostScript file name
)
-icl
fname (
input clustering name
)
The
-o
fname
option controls the name of
the file in which the reachability values are written. By
default these values are written to STDOUT.
If -ps fname is supplied the program will additionally output a visualisation of the reachability landscape plot in a PostScript file.
It is possible, in addition to -ps , to specify a clustering with -icl fname . Each vertical bar in the landscape plot will be coloured according to cluster membership, that is, nodes in the same cluster will have the same colour. This can be a useful way to visualise separation properties of clusterings.
-psx
fname (
scaling factor x axis
)
-psy
fname (
scaling factor y axis
)
--ps-labels
(
show identifiers in PS output
)
-ps-rows
<num> (
split reachability plot into
<num> rows
)
By default the PostScript output will be scaled to fit onto
an A3 page. The scaling options
-psx
and
-psy
can be used as additional scaling factors. By default these
are set
1.0
.
The --ps-labels can be used to annotate each vertical bar in the landscape plot with the mcl-edge identifier of the corresponding node.
The -ps-rows option sets the number of rows. This is the primary option affect the width of a bar.
AUTHOR
Stijn van Dongen.
SEE ALSO
mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.