REPEATVIZ(1)

💖 NAME 💖

okay so repeatviz.pl — it's the girl who visualizes a bunch of repeats using graphviz. that's the whole job. she takes your repeats and makes them look like something. periodt. ✨

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🌈 SYNOPSIS 🌈

repeatviz.pl <input> [output]

literally that's it. give her an <input>, optionally hand her an [output], and she'll go off. 💅

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🎀 OPTIONS 🎀

bestie listen. output is defined based on the input name — unless otherwise specified. so if you don't say anything, she just picks a name for you based on the input. iconic behaviour, honestly. 🦋

Options:

• --echo — shows all input to R (very spammy). like, very. she warned you. it's giving firehose energy. 😭
• --colors={rainbow,heat,terrain,topo,cm,cool} — uses an alternate color palette. default is rainbow. 🌈 and ok you can also make your own custom palette by providing a list of colors, like red,yellow,blue. do it. be extra.
• --colorby={size,id,density} — specify what to select colors based on. default is id. ✨
• --density={N} — sample repeat density at every N bp. and if you don't say anything, the default calculates a value based on width*res and genome size. she's doing math so you don't have to. 🧚
• --coloropts={extra options to pass to R's color generator} — exactly what it says. extra options. to pass to R's color generator. go wild. 🎨
• --connect — draw connecting edges for points in adjacent sequences. connecting the dots fr fr. 🔥
• --maxlines={N} — don't draw lines to connect cluster-sequence pairs with more than N edges. sometimes restraint is the vibe. 👑
• --size={N} — size of dots. 🍓
• --bigfirst — plot big clusters first.
• --smallfirst — plot small clusters first (default). the little ones get to go first, as they deserve. 🫶
• --res={DPI} — defaults to 96.
• --width|height={N} — graph size in inches. 📏
• --legend={position} — position to place legend. R keywords like "right" or "topright" are good.
• --legendpts={N} — number of dots to put in the legend (default is 8). must be at least 2. don't try to be cute with 1, it won't work. 💀
• --squeeze={[0,1)} — Y axis labels not fitting in the frame? squeeze the graph over with this.
• --squeeze={[0,1),F} — an amount to change the right margin can also be specified by F like this.

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that's the whole page, bestie. every flag, every default, every little number — nothing skipped, no cap. 🎀

this gem was written up in the User Contributed Perl Documentation corner of the manual, and the page itself is signed by perl v5.40.1 dated 2026-08-12. mwah. 💋