MCXCLCF(1)

mcx clcf(1) — the USER COMMANDS era 💅

okay bestie, welcome to mcx clcf, a manual page in the USER COMMANDS section, and honestly? she's serving graph math realness. let's get into it 🫶

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✨ NAME ✨

mcx_clcf — compute the clustering coefficient of a graph. that's it. that's the whole job. iconic behavior 🌸

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🦋 SYNOPSIS 🦋

mcx clcf [options] [matrix-file]

okay so first things first: mcxclcf is not in actual fact a program. not me exposing the truth 😭. this manual page documents the behaviour and options of the mcx program when invoked in mode clcf. the options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes, and they're described in the mcx manual page. so like, go read that one too, iykyk 💜

and here's the full vibe, verbatim:

mcx clcf [-abc <fname> (specify label input)] [-imx <fname> (specify
matrix input)] [-tab <fname> (use tab file)] [-o <fname> (write to this
file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs
are used)] [-j <intj> (this job has index <intj>)] [--summary (return
mean clustering coefficient)] [-h (print synopsis, exit)] [--apropos
(print synopsis, exit)] [--version (print version, exit)]

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🌈 DESCRIPTION 🌈

mcx clcf computes the clustering coefficient of a graph. periodt. 🎀

the input graph/matrix, if you specify it with the -imx option, has to be in mcl matrix/graph format. you can use label input instead by using the -abc option. refer to mcxio(5) for a description of these two input formats — bestie, that page is your study guide, no skipping ✨

by default mcx diameter reads from STDIN and expects matrix format. to specify label input from STDIN use -abc -. that little dash is doing a lot of heavy lifting, respect her 💅

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💖 OPTIONS 💖

• -abc <fname> (label input) — the file name for input that is in label format. label girlies rise 🦋
• -imx <fname> (input matrix) — the file name for input. STDIN is assumed if not specified, so if you're lazy (valid), she'll just listen 🫶
• -o <fname> (output file) — the file name for output. STDOUT is the default output stream, aka the group chat is the default destination 💜
• -tab <fname> (use tab file) — this option causes the output to be printed with the labels found in the tab file. with -abc this option will, additionally, construct a graph only on the labels found in the tab file. if this option is used in conjunction with -imx the tab domain and the matrix domain are required to be identical. no mixing domains, that's the rule 😌
• --summary (return mean clustering coefficient) — by the default a 1-column table (with row names included) is output, one row for each node. this option causes the output of the average clustering coefficient only. so like, the TL;DR version 🌸
• -t <int> (use <int> threads)
• -J <intJ> (a total of <intJ> jobs are used)
• -j <intj> (this job has index <intj>)

computing clustering coefficients is time-intensive for large graphs. if you have multiple CPUs available consider using as many threads. additionally it is possible to spread the computation over multiple jobs/machines. these three options are described in the clmprotocols manual page. the following set of options, if given to as many commands, defines three jobs, each running four threads:

-t 4 -J 3 -j 0 -o out.0
-t 4 -J 3 -j 1 -o out.1
-t 4 -J 3 -j 2 -o out.2

the output can then be collected with

mcx collect --add-column -o out.all out.[0-2]

okay diva, distribute that workload, main character energy across three whole machines 🔥

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👑 SEE ALSO 👑

mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. the whole mcl family tree, obsessed 🌈

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that's the whole page bestie!! this one's mcx clcf, version 22-282, dated 9 Oct 2022 — go forth and cluster, you absolute icon 💖✨🦋