LDA.py

Create an LDA plot from sample-grouped OTU data. It is necessary to remove the header cell ‘#OTU ID’ before running this program.

usage: LDA.py [-h] -i BIOM_TSV -m MAP_FP -g GROUP_BY [GROUP_BY ...] -c COLOR_BY [--dpi DPI] [--save_lda_input SAVE_LDA_INPUT] [--plot_title PLOT_TITLE] [-o OUT_FP]

Required arguments

-i BIOM_TSV, --biom_tsv BIOM_TSV

Sample-OTU abundance table in TSV format with the arcsin sqrt transform already applied.

-m MAP_FP, --map_fp MAP_FP

Metadata mapping file.

Optional arguments

-g GROUP_BY [GROUP_BY ...], --group_by GROUP_BY [GROUP_BY ...]

Any mapping categories, such as treatment type, that will be used to group the data in the output iTol table. For example, one category with three types will result in three data columns in the final output. Two categories with three types each will result in six data columns. Default is no categories and all the data will be treated as a single group.

-c COLOR_BY, --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.

--dpi DPI

Set plot quality in Dots Per Inch (DPI). Larger DPI will result in larger file size.

--save_lda_input SAVE_LDA_INPUT

Save a CSV-format file of the transposed LDA-input table to the file specifed by this option.

--plot_title PLOT_TITLE

Plot title. Default is no title.

-o OUT_FP, --out_fp OUT_FP

The path and file name to save the plot under. If specified, the figure will be saved directly instead of opening a window in which the plot can be viewed before saving.

-h, --help

Show the help message and exit.