mcxalter(1)

💅 NAME 💅

mcxalter — bestie, this is your little network-transformation station ✨ it does various network transformations, that's literally the whole vibe.

---

✨ SYNOPSIS ✨

mcxalter [-imx <fname> (specify matrix/graph input)] [-abc <fname>
(specify label input)] [-tab <fname> (use tab file)] [-icl <fname>
(specify cluster input)] [--block (use within-cluster edges)] [--blockc
(use between-cluster edges)] [-o <fname> (output)] [-tf spec (apply tf-
spec to input matrix)]

---

🦋 DESCRIPTION 🦋

Okay so this utility supplies various transformations of networks. That's it, that's the whole job description. She transforms, she serves, she goes home. 👑

---

🌸 OPTIONS 🌸

• -abc <fname> (label input) — the filename for your input, and it needs to be in label format. That's the tea.
• -imx <fname> (input matrix) — the filename for your input when it's in mcl native matrix format. Different format, same energy.
• -tab <fname> (use tab file) — this one makes the output print with the labels it found in the tab file. And with -abc it will additionally construct a graph only on the labels found in the tab file, no cap. 🎀 If you use this together with -imx, then the tab domain and the matrix domain are required to be identical — like, non-negotiable bestie, they gotta match.
• -icl <fname> (specify cluster input) — read in a cluster file so it can be used with either --block or --blockc. 🫶
• --block (use within-cluster edges) — removes the between-cluster edges from the network. Lowkey important: this happens first, before any of the other transformations take effect.
• --blockc (use between-cluster edges) — removes the within-cluster edges from the network. And same thing here — it goes first, before the other transformations take effect.
• -tf <tf-spec> (transform input matrix values) — transforms the input matrix values following the syntax described over in mcxio(5). Go read it, iykyk.
• -o fname (output file) — output file. That's where the magic lands. ✨

---

💜 AUTHOR 💜

Stijn van Dongen. (An icon, honestly. 🙈)

---

🌈 SEE ALSO 🌈

mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. Go read the whole family tree, bestie, it's giving ✨lore✨.

---

And that's a wrap, gorgeous 💖 this was mcxalter version 22-282, dated 9 Oct 2022. Slay, stay transformed, and don't forget to hydrate 🍓