CLMCLOSE(1)

💖 NAME 💖

clm_close — fetch connected components from graphs or subgraphs 🦋

okay so first things first, bestie: clmclose is not actually a program, no cap. This manual page documents the behaviour and options of the clm program when you invoke it in mode close. And the options -h, --apropos, --version, -set, --nop are accessible in all clm modes — they're described over in the clm manual page, so go peek there, iykyk 💅

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✨ SYNOPSIS ✨

clm close -imx <fname> [options]

clm close -imx fname (specify matrix input) -abc fname (specify label
input) -dom fname (input domain/cluster file) [-o fname (output file)]
[--is-undirected (trust input graph to be undirected)] [-levels
LO/STEP/HI[/prefix] (write cluster size distribution for each cutoff)]
[-levels-norm num (divide each level by num to define cutoff)] [--write-
count (output component count)] [--write-sizes (output component sizes
(default))] [--write-size-counts (output compressed list of component
sizes)] [--write-cc (output components as clustering)] [--write-block
(output graph restricted to -dom argument)] [--write-blockc (output graph
complement of -dom argument)] [-cc-bound num (select components with size
at least num)] [--sl (output single linkage tree as list of joins (for
-imx input))] [-write-sl-list fname (write list of join order with
weights)] [-tf spec (apply tf-spec to input matrix)] [-h (print synopsis,
exit)] [--apropos (print synopsis, exit)] [--version (print version,
exit)]

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🌈 DESCRIPTION 🌈

Use clm close to fetch the connected components from a graph. Different output modes are supported — see below, bestie 👀

In matrix mode (i.e. using the -imx option) the output you get back with --write-cc can be used in conjunction with mcxsubs to retrieve individual subgraphs corresponding to connected components. it's giving very useful, fr fr 🌸

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🎀 OPTIONS 🎀

• -abc <fname> (label input) — the file name for input that is in label format.
• -imx <fname> (input matrix) — the file name for input that is in mcl native matrix format.
• -o fname (output file) — specify the file where output is sent to. The default is STDOUT. periodt.
• -dom fname (input domain/cluster file) — if this option is used, clm close will, as a first step, for each of the domains in file fname retrieve the associated subgraph from the input graph. These are then further decomposed into connected components, and the program will process these in the normal manner. slay 💅
• --write-count (output component count)
• --write-sizes (output component sizes (default))
• --write-size-counts (output compressed list of component sizes)
• --write-cc (output components as clustering)
• --write-block (output graph restricted to -dom argument)
• --write-blockc (output graph complement of -dom argument)

The default behaviour is currently to output the sizes of the connected components. It is also possible to simply output the number of components with --write-count, to write a counted list of sizes with --write-size-counts, or to write the components as a clustering in mcl format with -write-cc. Even more options exist: it is possible to output the restriction of the input graph to a domain, or to output the complement of this restriction. so many vibes, pick your main character 😌✨

• -levels LO/STEP/HI[/prefix] (write cluster size distribution for each cutoff)
• -levels-norm num (divide each level by num to define cutoff)

Use -levels to inspect the cluster size distribution at various cut-offs by specifying a triplet of numbers (separated by forward slashes), the first of which is the starting point, the second is the step size, and the third is the end point. If a fourth argument (preceded by another slash) is given, all clusterings are written to a file based on the supplied argument as file name prefix. The cut-off can be further varied by the argument to -levels-norm. 🍓

• --sl (output single linkage tree as list of joins (for -imx input))
• -write-sl-list fname (write list of join order with weights)

A primary use case for this is to apply single link clustering to the rcl (restricted contingency linkage) graph that is output by clm vol with its write-rcl option. This rcl graph encodes a consensus clustering derived from the multiple clusterings that are given to clm vol. 🧚

The output (save with -o or UNIX redirection) can be supplied to rcl-res.pl with a list of varying resolution parameters to produce a small number of nested clusterings. The resolution parameters (second and subsequent arguments) to rcl-res.pl are set sizes; For each of the supplied resolutions res the script will descend the tree as long as the current node has some split below it where both clusters are of size at least res. Note that the resulting clustering may still have smaller clusters and singletons (resulting from other splits). 💜

The mcl distribution has an example script graphs/rcl-example.sh that illustrates the different steps. iconic 🌟

• --is-undirected (omit graph undirected check) — with this option the transformation to make sure that the input is undirected is omitted. This will be slightly faster. Using this option while the input is directed may lead to erronenous results. 😭 (yes bestie, that's a typo in the original manpage, we love her anyway)

⚠️ heads up: this one is a trust me bro option. If the input is actually directed and you use it, your results can be wrong. no cap.

• -cc-bound num (select components with size at least num) — transform the input matrix values according to the syntax described in mcxio(5). 🫶

psst — -tf spec (apply tf-spec to input matrix) shows up in the synopsis up there but gets no description of its own down here. just so you're not confused, bestie 💖

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👑 AUTHOR 👑

Stijn van Dongen. 🎀

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💀 SEE ALSO 💀

mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. go read it, it's the whole squad 🌈

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and that's the whole page, bestie!! 💖 this was clm close version 22-282, dated 9 Oct 2022 — thanks for scrolling all the way down, mwah 🫶✨🌸