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