plot_rank_abundance_graph.py – plot rank-abundance curve

Description:

Plot a set of rank-abundance graphs from an OTU table and a set of sample names. Multiple graphs will be plotted into the same figure, in order to allow for an easy comparison across samples.

Usage: plot_rank_abundance_graph.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

Path to the input OTU table (i.e., the output from make_otu_table.py)

-s, --sample_name

Name of the sample to plot. Use “*” to plot all.

-o, --result_fp

Path to store resulting figure file. File extension will be appended if not supplied (e.g.: rankfig -> rankfig.pdf). Additionally, a log file rankfig_log.txt will be created

[OPTIONAL]

-a, --absolute_counts

Plot absolute abundance values instead of relative [default: False]

-n, --no_legend

Do not draw a legend [default: False]

-x, --x_linear_scale

Draw x axis in linear scale [default: False]

-y, --y_linear_scale

Draw y axis in linear scale [default: False]

-f, --file_type

Save plot using this image type. Choice of pdf, svg, png, eps [default: pdf]

Output:

Single graph example:

Plot the rank-abundance curve of one sample using a linear scale for the x_axis:

plot_rank_abundance_graph.py -i otu_table.biom  -s 'PC.354' -x -v -o single_plot.pdf

multiple graph example:

Plot the rank-abundance curve of several samples:

plot_rank_abundance_graph.py -i otu_table.biom  -s 'PC.354,PC.481,PC.636' -x -v -o multi_plot.pdf

multiple graph example:

Plot the rank-abundance curve of all samples in an OTU table:

plot_rank_abundance_graph.py -i otu_table.biom  -s '*' -x -f eps -v -o all_plot.eps