LEFSE_PLOT_CLADOGRAM.PY(1)

📦 version 1.1.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 lefse_plot_cladogram.py 💖

okay bestie, welcome to the LEFSE_PLOT_CLADOGRAM.PY(1) page, straight outta the User Commands section. this is the whole vibe, no cap 💅

✨ NAME ✨

lefse_plot_cladogram.py — determine features of organisms, clades, taxonomic units, genes

like. she's a cladogram plotter. she determines the features. iconic behavior honestly 🦋

🌸 DESCRIPTION 🌸

the usage, verbatim, because I would never do you dirty:

lefse_plot_cladogram.py [-h] [--clade_sep CLADE_SEP] [--max_lev MAX_LEV] [--max_point_size MAX_POINT_SIZE] [--min_point_size MIN_POINT_SIZE] [--point_edge_width MARKEREDGEWIDTH] [--siblings_connector_width SIBLINGS_CONNECTOR_WIDTH] [--parents_connector_width PARENTS_CONNECTOR_WIDTH] [--radial_start_lev RADIAL_START_LEV] [--labeled_start_lev LABELED_START_LEV] [--labeled_stop_lev LABELED_STOP_LEV] [--abrv_start_lev ABRV_START_LEV] [--abrv_stop_lev ABRV_STOP_LEV] [--expand_void_lev EXPAND_VOID_LEV] [--class_legend_vis CLASS_LEGEND_VIS] [--colored_connector COLORED_CONNECTORS] [--alpha ALPHA] [--title TITLE] [--sub_clade SUB_CLADE] [--title_font_size TITLE_FONT_SIZE] [--right_space_prop R_PROP] [--left_space_prop L_PROP] [--label_font_size LABEL_FONT_SIZE] [--background_color {k,w}] [--colored_labels {0,1}] [--class_legend_font_size CLASS_LEGEND_FONT_SIZE] [--dpi DPI] [--format {png,svg,pdf}] [--all_feats ALL_FEATS] INPUT_FILE OUTPUT_FILE

Cladoplot ✨ that's it, that's the one-liner.

🎀 positional arguments 🎀

the two things you literally cannot skip, main character energy only:

  • INPUT_FILE — tab delimited input file. tabs. delimited. she's specific 🍓
  • OUTPUT_FILE — the file for the output image. where the art goes 🖼️

💅 optional arguments 💅

heads up babe: a bunch of these show up in the usage with zero explanation attached. that's not me gatekeeping, that's genuinely all the manpage gives us. iykyk 🙈
  • -h, --help — show this help message and exit. the classic. the icon. the moment you type it, she explains herself and dips 👑
  • --clade_sep CLADE_SEP — no description in the original, just vibes and a value
  • --max_lev MAX_LEV — same deal, she takes a MAX_LEV
  • --max_point_size MAX_POINT_SIZE — takes a MAX_POINT_SIZE
  • --min_point_size MIN_POINT_SIZE — takes a MIN_POINT_SIZE
  • --point_edge_width MARKEREDGEWIDTH — takes a MARKEREDGEWIDTH (yes, that's the metavar, we don't question it)
  • --siblings_connector_width SIBLINGS_CONNECTOR_WIDTH — takes a SIBLINGS_CONNECTOR_WIDTH
  • --parents_connector_width PARENTS_CONNECTOR_WIDTH — takes a PARENTS_CONNECTOR_WIDTH
  • --radial_start_lev RADIAL_START_LEV — takes a RADIAL_START_LEV
  • --labeled_start_lev LABELED_START_LEV — takes a LABELED_START_LEV
  • --labeled_stop_lev LABELED_STOP_LEV — takes a LABELED_STOP_LEV
  • --abrv_start_lev ABRV_START_LEV — takes an ABRV_START_LEV
  • --abrv_stop_lev ABRV_STOP_LEV — takes an ABRV_STOP_LEV
  • --expand_void_lev EXPAND_VOID_LEV — takes an EXPAND_VOID_LEV
  • --class_legend_vis CLASS_LEGEND_VIS — takes a CLASS_LEGEND_VIS
  • --colored_connector COLORED_CONNECTORS — takes COLORED_CONNECTORS
  • --alpha ALPHA — takes an ALPHA
  • --title TITLE — takes a TITLE
  • --sub_clade SUB_CLADE — takes a SUB_CLADE
  • --title_font_size TITLE_FONT_SIZE — takes a TITLE_FONT_SIZE
  • --right_space_prop R_PROP — takes an R_PROP
  • --left_space_prop L_PROP — takes an L_PROP
  • --label_font_size LABEL_FONT_SIZE — takes a LABEL_FONT_SIZE
  • --background_color {k,w} — set the color of the background. pick your palette bestie, it's k or w 🌈
  • --colored_labels {0,1} — draw the label with class color (1) or in black (0). so 1 is the colorful slay, 0 is the black-on-black minimalist moment 🖤
  • --class_legend_font_size CLASS_LEGEND_FONT_SIZE — takes a CLASS_LEGEND_FONT_SIZE
  • --dpi DPI — takes a DPI
  • --format {png,svg,pdf} — the format for the output file. three choices, all valid, all gorgeous ✨
  • --all_feats ALL_FEATS — takes an ALL_FEATS

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. absolute legend, we stan 🫶

and that's the whole page babes 💖 this was lefse_plot_cladogram.py version 1.1.2, dated September 2021, served up in the LEFSE_PLOT_CLADOGRAM.PY(1) section. go forth and cladogram, periodt 🌟

📦 where this page comes from