LEFSE_PLOT_FEATURES.PY(1)

💖 LEFSE_PLOT_FEATURES.PY 💖

okay bestie, welcome to lefse_plot_features.py — it's a User Command and it lives in section 1 of the manual, which is just fancy speak for "type it in your terminal, babe". no cap. 🫶

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✨ NAME ✨

lefse_plot_features.py — determine features of organisms, clades, taxonomic units, genes. it's giving taxonomy but make it a plot. 🌈🦋

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🎀 DESCRIPTION 🎀

so the way you run it is literally this, and I'm putting it in a code block so you don't have to squint at wrapped text like it's a group chat at 2am:

lefse_plot_features.py [-h] [--width WIDTH] [--height HEIGHT]
                       [--top TOP] [--bot BOT]
                       [--title_font_size TITLE_FONT_SIZE] [--class_font_size CLASS_FONT_SIZE]
                       [--class_label_pos {up,down}] [--subcl_mean {y,n}] [--subcl_median {y,n}]
                       [--font_size FONT_SIZE] [-n flt] [--format {png,pdf,svg}] [-f {all,diff,one}]
                       [--feature_name FEATURE_NAME] [--feature_num FEATURE_NUM]
                       [--archive {zip,none}] [--background_color {k,w}] [--dpi DPI]
                       INPUT_FILE INPUT_FILE OUTPUT_FILE

Cladoplot 💅

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🌸 positional arguments 🌸

these ones you just... hand over. no dashes, no ceremony, just vibes.

• INPUT_FILE — dataset files. yep, the first one. 🍓
• INPUT_FILE — LEfSe output file. yep, the second one, and I know it has the exact same name as the first, I'm not the one who named it, bestie. 😭
• OUTPUT_FILE — the file for the output. and specifically: it's the zip file if an archive is required, and the output directory otherwise. so it switches personalities depending on your flags, main character energy honestly. 👑

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⭐ optional arguments ⭐

• -h, --help — show this help message and exit. the classic. always there for you. 🫶
• --width WIDTH — sets the width. (no description in the original, she's mysterious like that 🙈)
• --height HEIGHT — sets the height. (also mysterious. iconic behaviour.)
• --top TOP — set maximum y limit (-1.0 means automatic limit). let the plot decide its own ceiling, slay ✨
• --bot BOT — set minimum y limit (default 0.0, -1.0 means automatic limit). floor check, but make it data 💅
• --title_font_size TITLE_FONT_SIZE — title font size. make it big, make it bold, make it a moment 🎀
• --class_font_size CLASS_FONT_SIZE — class font size.
• --class_label_pos {up,down} — where the class labels sit. up or down. choose your fighter.
• --subcl_mean {y,n} — y or n, bestie.
• --subcl_median {y,n} — y or n again.
• --font_size FONT_SIZE — the general font size.
• -n flt — unused. yes literally, the manpage says unused. she's just standing there. 💀
• --format {png,pdf,svg} — the format for the output file. pick your aesthetic: png, pdf, or svg. 🌈
• -f {all,diff,one} — whether to plot all features (all), only those differentially abundant according to LEfSe (diff), or only one — the one given with --feature_name (one). this is the whole personality of the script fr fr.
• --feature_name FEATURE_NAME — The name of the feature to plot (levels separated by .). yes, dots, not spaces, not slashes, dots. iykyk. 💅
• --feature_num FEATURE_NUM — The number of the feature to plot.
• --archive {zip,none} — zip or none, choose wisely because this decides whether your OUTPUT_FILE is a zip file or a directory. no pressure. 🫶
• --background_color {k,w} — set the color of the background. k or w. that's the whole menu, babes.
• --dpi DPI — the dpi. crank it if you want it crispy. 🔥

heads up bestie: several of these options ship with no description at all in the original manual. I'm not out here inventing lore for them, so they stay cute and unexplained. we respect the source. 🧚

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👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. king behaviour, honestly. 💖

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and that's the whole page, bestie — lefse_plot_features.py version 1.1.2, dated September 2021, straight out of the Debian-verse. go plot something gorgeous. periodt. ✨🦋💅