LEFSE_PLOT_FEATURES.PY

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}

wheter 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.