CNVKIT_HEATMAP(1)

✨ CNVKIT_HEATMAP ✨

okay bestie, welcome to the cnvkit_heatmap page 💖 (that's the manual page name, it lives in section 1 of the manual, iykyk). This is the glow-up guide to plotting copy number for a whole squad of samples as one gorgeous heatmap 🌈

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🌸 NAME 🌸

cnvkit_heatmap — Plot copy number for multiple samples as a heatmap. no cap, that's literally the whole job 🎀

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🦋 DESCRIPTION 🦋

Here's the vibe check — the usage looks like this:

cnvkit.py heatmap [-h] [-c CHROMOSOME] [-y]
       [-x {m,y,male,Male,f,x,female,Female}]
              [--no-shift-xy] [-o FILENAME] [-b] [-d] [-v] [--delimit-samples]
              [-t TITLE] filenames [filenames ...]

💅 positional arguments:

• filenames — the sample coverages you're feeding in, either as raw probes (.cnr) or segments (.cns). give me the data bestie 🫶

👑 options:

• -h, --help — show this help message and exit. the classic. the icon. press it when you're lost 💀
• -c CHROMOSOME, --chromosome CHROMOSOME — pick a chromosome (like 'chr1') or a chromosomal range (like 'chr1:2333000-2444000') to display. If you hand over a range, all the targeted genes inside that range get shown — unless --gene/-g was already given. so like, don't double-dip 💖
• -y, --male-reference, --haploid-x-reference — assume the inputs were normalized to a male reference. Which means: female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX. it's giving "know your normalization" 🧚
• -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} — specify the chromosomal sex of all the given samples as male or female. Default: guess each sample from coverage of X and Y chromosomes ✨ (the default is lowkey doing detective work for you)
• --no-shift-xy — don't adjust the X and Y chromosomes according to sample sex. hands off 🔥
• -o FILENAME, --output FILENAME — Output PDF file name. name your baby 💖

🎨 Plot aesthetics:

• -b, --by-bin — plot data x-coordinates by bin indices instead of genomic coordinates. Every bin gets shown with equal width, no blank regions show up at all, and the x-axis values indicate bin number (within chromosome) instead of genomic position. equal widths only, we love a fair fight 👑
• -d, --desaturate — tweak color saturation to focus on the significant changes. muted palette, loud findings 🌸
• -v, --vertical — plot the heatmap with samples as the X-axis (instead of the Y-axis). rotate the whole situation, main character energy 🔄
• --delimit-samples — add an horizontal delimitation line between each sample. boundaries, bestie 🎀
• -t TITLE, --title TITLE — Plot title. Default: Range if provided, otherwise none. so if you gave a range, you get a title for free ✨

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no cap: every flag above is doing real work, so read the one you're about to type before you type it. especially the sex/reference ones — they change what your X and Y even mean 💀

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that's the whole page, babe — go make something pretty and correct 🦋💖

signing off: this was cnvkit.py heatmap version 0.9.10, dated July 2023, and yes that's the version that was serving looks when this manpage was written 👑✨