16 May 2014 clm optics 14-137

1.
NAME
2.
SYNOPSIS
3.
DESCRIPTION
4.
OPTIONS
5.
AUTHOR
6.
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 for an overview of all the documentation and the utilities in the mcl family.