CLMIMAC(1)

✨ clm imac — the manual page, but make it make sense ✨

okay bestie, sit down, grab a boba, because we're talking about clm imac — and no, before you ask, this is not in actual fact a program. 😭

clmimac isn't a real binary out here living its life. This page is literally just documenting how the clm program behaves when you invoke it in mode imac. That's it, that's the vibe. 💅

also real quick, the options -h, --apropos, --version, -set, and --nop are available in all clm modes, so they get their own dedicated page — go read the clm manual page for those. 🫶

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🌸 NAME 🌸

clm_imac — Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

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🎀 SYNOPSIS 🎀

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)]

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🦋 DESCRIPTION 🦋

So what does it even do? clm imac interprets matrices as clusterings — specifically the matrices that mcl spits out when you use mcl's -dump ite option. ✨

But listen. Use clm imac only if you have a special reason, okay? The normal way to use mcl is to do multiple runs with varying -I parameters and then just use the clusterings that mcl itself outputs. That's the standard main-character path. 👑

So when would you want this instead? Two reasons, bestie:

• You're interested in clusterings with overlap. Early MCL iterands generally induce clusterings that possess overlap, and that's kinda their whole thing. 💖
• You wanna investigate how the cluster structure associated with the MCL process evolves over time. It's giving time-lapse documentary energy. 🌈

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💖 OPTIONS 💖

• -imx fname (input file) — the input file, which is presumably an MCL iterand that came from the mcl option -dump ite. 📥
• -strict num (in 0..1) — higher values (up until 1) will thin out the DAG that clm imac constructs. The default value is 0.00001, which yields the full DAG. 🌱
• -o fname (file name/stem) — write to the file named fname. 📝
• -dag fname (output DAG) — write the DAG (directed acyclic graph) constructed from the input to a 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 by increasing size, decreasing size, lexicographically by the indices they contain, or just use the clustering exactly as obtained from the interpretation routine. Pick your fighter. 💅
• -overlap mode (overlap mode) — okay so this one's a whole vibe:
  • mode cut — remove any overlap by allocating the nodes in overlap to the first cluster in which they were found. ✂️
  • mode keep — leaves overlap unchanged. untouched. unbothered. 🧘
  • mode split — results in overlapping parts being excised and introduced as clusters in their own right. glow-up via separation. 🌟

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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 explore, iykyk. 📚

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and that's the whole page, bestie!! 🎀 this was clm imac version 22-282, dated 9 Oct 2022, living under the USER COMMANDS section of the manual. slay, stay clustered, and remember: no cap, just -dump ite. 💜✨