LDA_bubble.py

This script returns LDA plots, with samples/dots sized by relative abundances of input OTU(s).

usage: LDA_bubble.py [-h] -i OTU_TABLE -m MAP_FP -g GROUP_BY -c COLOR_BY -ids OTU_IDS_FP [-dm DIST_MATRIX_FILE] [--save_lda_input SAVE_LDA_INPUT] [-od OUTPUT_DIR] [--scale_by SCALE_BY] [-s SAVE_AS] [--ggplot2_style] [-v]

Required arguments

-i OTU_TABLE, --otu_table OTU_TABLE

Input biom file format OTU table.

-m MAP_FP, --map_fp MAP_FP

Metadata mapping file.

-g GROUP_BY, --group_by GROUP_BY

A column name in the mapping file containing categorical values that will be used to identify groups. Each sample ID must have a group entry. 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.

-ids OTU_IDS_FP, --otu_ids_fp OTU_IDS_FP

Path to a file containing one OTU ID per line. One plot will be created for each OTU.

Optional arguments

-dm DIST_MATRIX_FILE, --dist_matrix_file DIST_MATRIX_FILE

Input distance matrix file.

--save_lda_input SAVE_LDA_INPUT

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

-od OUTPUT_DIR, --output_dir OUTPUT_DIR

The directory to save the LDA bubble plots to. By default, plots will be saved in current working directory.

--scale_by SCALE_BY

Species relative abundance is multiplied by this factor in order to make appropriate visible bubbles in the output plots. Default scaling is 1000.

-s SAVE_AS, --save_as SAVE_AS

The type of image file for LDA plots. By default, plots will be saved in ‘svg’ format.

--ggplot2_style

Apply ggplot2 styling to the figure.

-v, --verbose

Displays species name as each is being plotted and stored to disk.

-h, --help

Show the help message and exit