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#!/usr/bin/env python
# File created on 16 Aug 2010
from __future__ import division
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from qiime.util import get_tmp_filename
from qiime.plot_rank_abundance_graph import plot_rank_abundance_graphs
from qiime.util import parse_command_line_parameters, get_options_lookup, \
create_dir
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = "plot rank-abundance curve"
script_info['script_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."
script_info['script_usage'] = [("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.txt -s 'Sample1' -x -v"),
("multiple graph example",
"Plot the rank-abundance curve of several sample:",
"plot_rank_abundance_graph.py -i otu_table.txt -s 'Sample1,Sample3,Sample5' -x -v"),
("multiple graph example",
"Plot the rank-abundance curve of all samples in an OTU table:",
"plot_rank_abundance_graph.py -i otu_table.txt -s '*' -x -f eps -v"),
]
script_info['output_description']= ""
script_info['required_options'] = [
options_lookup['otu_table_as_primary_input'],
make_option('-s','--sample_name',help='name of the sample to plot. Use "*" to plot all.'),
]
#could basically allow all of matplotlib format here
file_types = ['pdf','svg','png','eps']
script_info['optional_options'] = [\
make_option('-o','--output_dir',help='name of output directory. '
+'[default: random]'),\
make_option('-a','--absolute_counts', help='plot absolute abundance values instead of '
+'relative [default: %default]', action='store_true', default=False),\
make_option('-n','--no-legend', action='store_true', default=False,
help='do not draw a legend [default: %default]'),\
make_option('-x','--x_linear_scale',help='draw x axis in linear scale '
+'[default: %default]',
action='store_true', default=False),\
make_option('-y','--y_linear_scale',help='draw y axis in linear scale '
+'[default: %default]',
action='store_true', default=False),
make_option('-f','--file_type',help='save plot using this image type. Choice of '+
', '.join(file_types) +' [default: %default]',
default='pdf')
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
#set up and create the outpurt dir
if opts.output_dir:
output_dir = opts.output_dir
else:
output_dir = get_tmp_filename(tmp_dir='./', prefix='rank_abundance_', suffix='')
create_dir(output_dir, fail_on_exist=True)
if opts.verbose:
log_fh = open(output_dir+"/plot_rank_abundance_log.txt",'w')
log_fh.write("OTU table file: %s\n"% opts.otu_table_fp)
log_fh.write("sample names: %s\n" % opts.sample_name)
else:
log_fh=None
plot_rank_abundance_graphs(opts.sample_name, open(opts.otu_table_fp,"U"),
output_dir, opts.file_type,
opts.absolute_counts, opts.x_linear_scale,
opts.y_linear_scale, opts.no_legend, log_fh)
if __name__ == "__main__":
main()
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