CNVKIT_DIAGRAM(1)

✨ NAME ✨

cnvkit_diagram — draw copy number (log2 coverages, segments) on chromosomes as a diagram 💅

okay so real quick, bestie: this is the cnvkit_diagram(1) page, and here's the tea 🫖

If both the raw probes and the segments are given, it shows them side-by-side on each chromosome — segments on the left side, probes on the right side. Iconic layout, no cap.

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💖 DESCRIPTION 💖

Here's the whole vibe, in usage form:

usage: cnvkit.py diagram [-h] [-s SEGMENT] [-c CHROMOSOME] [-t THRESHOLD]
                         [-m MIN_PROBES] [-y]
                         [-x {m,y,male,Male,f,x,female,Female}] [--no-shift-xy] [-o FILENAME] [--title TITLE] [--no-gene-labels] [filename]

That's the entire shape of the thing. Let's break it down, babe 🌸

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🎀 positional arguments 🎀

• filename — your processed coverage data file (*.cnr), aka the output of the fix sub-command. That's the glow-up file right there 💖

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🔥 options 🔥

• -h, --help — shows this help message and then dips. bye 👋
• -s SEGMENT, --segment SEGMENT — the segmentation calls (.cns), which is the output of the segment command. feed it the segments and it will slay
• -c CHROMOSOME, --chromosome CHROMOSOME — the chromosome to display, e.g. 'chr1'. and no, you can't do a chromosomal range here — no range allowed, periodt 🚫
• -t THRESHOLD, --threshold THRESHOLD — the copy number change threshold used to label genes. [Default: 0.5]
• -m MIN_PROBES, --min-probes MIN_PROBES — the minimum number of covered probes needed before a gene gets labeled. [Default: 3]
• -y, --male-reference, --haploid-x-reference — assume the inputs were normalized to a male reference. so basically: female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX. pick your fighter ⚔️
• -x {m,y,male,Male,f,x,female,Female}, --sample-sex {m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female} — tell it the sample's chromosomal sex, male or female. (Otherwise it just guesses from the X and Y coverage. lowkey impressive of it, honestly 🙈)
• --no-shift-xy — don't adjust the X and Y chromosomes according to sample sex. hands off the X and Y, thank you 💅
• -o FILENAME, --output FILENAME — the output PDF file name. that's your final look, bestie 📄

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🌸 Plot aesthetics 🌸

this section is literally just about making it pretty, which is of course the most important part 💖

• --title TITLE — the plot title. [Default: sample ID, from filename or -i]
• --no-gene-labels — disables the gene_name labels on the plot. super useful when a lot of CNV were called and the labels are all fighting for the aux cord 😭

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ngl bestie, if your plot is a chaotic mess of overlapping gene names, --no-gene-labels is your best friend. she's giving clean.

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that's the whole page, you ate it, go draw some chromosomes 🦋

signing off with love from cnvkit.py diagram 0.9.10, dated July 2023 💜✨