diversity.py¶
Calculate the alpha diversity of a set of samples using one or more metrics and output a kernal density estimator-smoothed histogram of the results.
usage: diversity.py [-h] [-d DIVERSITY [DIVERSITY ...]] [--plot_title PLOT_TITLE] [--image_type IMAGE_TYPE] [--save_calculations SAVE_CALCULATIONS] [--show_significance] [--show_available_metrics] -m MAP_FILE -i BIOM_FP -c CATEGORY --color_by COLOR_BY -o OUT_DIR
Required arguments¶
-
-m
MAP_FILE
,
--map_file
MAP_FILE
¶ QIIME mapping file.
-
-i
BIOM_FP
,
--biom_fp
BIOM_FP
¶ BIOM table file name
-
-c
CATEGORY
,
--category
CATEGORY
¶ Specific category from the mapping file.
-
--color_by
COLOR_BY
¶ A column name in the mapping file containing hexadecimal (#FF0000) color values that will be used to color the groups. Each sample ID must have a color entry.
-
-o
OUT_DIR
,
--out_dir
OUT_DIR
¶ The directory all plots will be saved to.
Optional arguments¶
-
-h
,
--help
¶
show this help message and exit
-
-d
DIVERSITY [DIVERSITY ...]
,
--diversity
DIVERSITY [DIVERSITY ...]
¶ The alpha diversity metric. Default value is ‘shannon’, which will calculate the Shannon entropy. Multiple metrics can be specified (space separated). The full list of metrics is available at: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.
-
--plot_title
PLOT_TITLE
¶ The name of a PDF file the pathway map will be written to.
-
-p
IMAGE_TYPE
,
--image_type
IMAGE_TYPE
¶ The type of image to save: PNG, SVG, etc.
-
--save_calculations
SAVE_CALCULATIONS
¶ Path and name of text file to store the calculated diversity metrics.
-
--show_significance
¶
Display significance testing results. The results will be shown by default.
-
--show_available_metrics
¶
Supply this parameter to see which alpha diversity metrics are available for usage. No calculations will be performed if this parameter is provided.