.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH LEFSE_PLOT_FEATURES.PY "1" "September 2021" "lefse_plot_features.py 1.1.2" "User Commands"
.SH NAME
lefse_plot_features.py \- determine features of organisms, clades, taxonomic units, genes
.SH DESCRIPTION
usage: lefse_plot_features.py [\-h] [\-\-width WIDTH] [\-\-height HEIGHT]
.TP
[\-\-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
.PP
Cladoplot
.SS "positional arguments:"
.TP
INPUT_FILE
dataset files
.TP
INPUT_FILE
LEfSe output file
.TP
OUTPUT_FILE
the file for the output (the zip file if an archive is
required, the output directory otherwise)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.HP
\fB\-\-width\fR WIDTH
.HP
\fB\-\-height\fR HEIGHT
.TP
\fB\-\-top\fR TOP
set maximum y limit (\fB\-1\fR.0 means automatic limit)
.TP
\fB\-\-bot\fR BOT
set minimum y limit (default 0.0, \fB\-1\fR.0 means automatic
limit)
.HP
\fB\-\-title_font_size\fR TITLE_FONT_SIZE
.HP
\fB\-\-class_font_size\fR CLASS_FONT_SIZE
.HP
\fB\-\-class_label_pos\fR {up,down}
.HP
\fB\-\-subcl_mean\fR {y,n}
.HP
\fB\-\-subcl_median\fR {y,n}
.HP
\fB\-\-font_size\fR FONT_SIZE
.TP
\fB\-n\fR flt
unused
.TP
\fB\-\-format\fR {png,pdf,svg}
the format for the output file
.TP
\fB\-f\fR {all,diff,one}
whether to plot all features (all), only those
differentially abundant according to LEfSe or only one
(the one given with \fB\-\-feature_name\fR)
.TP
\fB\-\-feature_name\fR FEATURE_NAME
The name of the feature to plot (levels separated by
\&.)
.TP
\fB\-\-feature_num\fR FEATURE_NUM
The number of the feature to plot
.HP
\fB\-\-archive\fR {zip,none}
.TP
\fB\-\-background_color\fR {k,w}
set the color of the background
.HP
\fB\-\-dpi\fR DPI
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.