LDA.py

This script calculates and returns LDA plots based on normalized relative abundances or distance matrices (for e.g. unifrac distance matrix).

usage: LDA.py [-h] -m MAP_FP -g GROUP_BY [-c COLORS] [-ot OTU_TABLE] [-dm DIST_MATRIX_FILE] [--save_lda_input SAVE_LDA_INPUT] [--plot_title PLOT_TITLE] [-o OUT_FP] [-d {2,3}] [--z_angles Z_ANGLES Z_ANGLES] [--figsize FIGSIZE FIGSIZE] [--font_size FONT_SIZE] [--label_padding LABEL_PADDING] [--annotate_points] [--ggplot2_style]

Required arguments

-m MAP_FP, --map_fp MAP_FP

Metadata mapping file.

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

Optional arguments

-c COLORS, --colors COLORS

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.

-ot OTU_TABLE, --otu_table OTU_TABLE

Input biom file format OTU table.

-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.

--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.

-d {2,3}, --dimensions {2,3}

Choose whether to plot 2D or 3D.

--z_angles Z_ANGLES Z_ANGLES

Specify the azimuth and elevation angles for a 3D plot.

--figsize FIGSIZE FIGSIZE

Specify the ‘width height’ in inches for LDA plots. By default, figure size is 14x8 inches.

--font_size FONT_SIZE

Sets the font size for text elements in the plot.

--label_padding LABEL_PADDING

Sets the spacing in points between the each axis and its label.

--annotate

If specified, each data point will be labeled with its sample ID. Currently, only works for 2D plots. Default is False.

--ggplot2_style

Apply ggplot2 styling to the figure. Default is False.

-h, --help

Show the help message and exit.

Workflow for generating LDA plots using PhyloToAST

Step 1 : Create an all-pairs distance matrix for your sample data using the beta_diversity.py QIIME script. Different distance metrics can be calculated here: bray_curtis, morisita_horn, kulczynski, and many others.

Step 2 : Users can use either diversity distance matrix file or BIOM format file to run LDA.py script with all relevant parameters. If a distance matrix file is provided, LDA will use the distance matrix as an input, otherwise it will calculate OTU relative abundances from input BIOM format file and run LDA based on OTU relative abundances.

Example plots

2D LDA plot based on relative abundances with 5 metadata categories [1].

LDA.py -i table.biom -m mapping.txt -g Condition -c Colors

Citation:

[1]	Dabdoub, S. M. et al. PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets. Sci. Rep. 6, 29123; doi: 10.1038/srep29123 (2016).