1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
.. _plot_rank_abundance_graph:
.. index:: plot_rank_abundance_graph.py
*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:** :file:`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 <./make_otu_table.html>`_)
-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
|
