table of contents
| LEFSE_PLOT_CLADOGRAM.PY(1) | User Commands | LEFSE_PLOT_CLADOGRAM.PY(1) |
NAME¶
lefse_plot_cladogram.py - determine features of organisms, clades, taxonomic units, genes
DESCRIPTION¶
usage: 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
positional arguments:¶
- INPUT_FILE
- tab delimited input file
- OUTPUT_FILE
- the file for the output image
optional arguments:¶
- -h, --help
- show this help message and exit
--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}
- set the color of the background
- --colored_labels {0,1}
- draw the label with class color (1) or in black (0)
--class_legend_font_size CLASS_LEGEND_FONT_SIZE
--dpi DPI
- --format {png,svg,pdf}
- the format for the output file
--all_feats 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.
| September 2021 | lefse_plot_cladogram.py 1.1.2 |