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