---
name: "lefse_plot_features.py"
section: "1"
platform: "linux"
package: "lefse"
version: "1.1.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lefse_plot_features.py"
---

# lefse\_plot\_features.py(1)

determine features of organisms, clades, taxonomic units, genes

## NAME

lefse\_plot\_features.py - determine features of organisms, clades, taxonomic units, genes

## DESCRIPTION

usage: 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

### positional arguments:

- INPUT\_FILE

  dataset files

- INPUT\_FILE

  LEfSe output file

- OUTPUT\_FILE

  the file for the output (the zip file if an archive is required, the output directory otherwise)

### optional arguments:

- **-h**, **--help**

  show this help message and exit

**--width** WIDTH

**--height** HEIGHT

- **--top** TOP

  set maximum y limit (**-1**.0 means automatic limit)

- **--bot** BOT

  set minimum y limit (default 0.0, **-1**.0 means automatic limit)

**--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

  unused

- **--format** {png,pdf,svg}

  the format for the output file

- **-f** {all,diff,one}

  whether to plot all features (all), only those differentially abundant according to LEfSe or only one (the one given with **--feature\_name**)

- **--feature\_name** FEATURE\_NAME

  The name of the feature to plot (levels separated by .)

- **--feature\_num** FEATURE\_NUM

  The number of the feature to plot

**--archive** {zip,none}

- **--background\_color** {k,w}

  set the color of the background

**--dpi** DPI

## AUTHOR

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