============= LDA_bubble.py ============= This script returns LDA plots, with samples/dots sized by relative abundances of input OTU(s). .. code-block:: bash 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 ^^^^^^^^^^^^^^^^^^^^ .. cmdoption:: -i OTU_TABLE, --otu_table OTU_TABLE Input biom file format OTU table. .. cmdoption:: -m MAP_FP, --map_fp MAP_FP Metadata mapping file. .. cmdoption:: -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. .. cmdoption:: -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. .. cmdoption:: -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 ^^^^^^^^^^^^^^^^^^ .. cmdoption:: -dm DIST_MATRIX_FILE, --dist_matrix_file DIST_MATRIX_FILE Input distance matrix file. .. cmdoption:: --save_lda_input SAVE_LDA_INPUT Save a CSV-format file of the transposed LDA-input table to the file specifed by this option. .. cmdoption:: -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. .. cmdoption:: --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. .. cmdoption:: -s SAVE_AS, --save_as SAVE_AS The type of image file for LDA plots. By default, plots will be saved in 'svg' format. .. cmdoption:: --ggplot2_style Apply ggplot2 styling to the figure. .. cmdoption:: -v, --verbose Displays species name as each is being plotted and stored to disk. .. cmdoption:: -h, --help Show the help message and exit