def get_coord(coord_fname, method="IQR"):
"""Opens and returns coords location matrix and metadata.
Also two spread matrices (+/-) if passed a dir of coord files.
If only a single coord file, spread matrices are returned as None.
"""
if not os.path.isdir(coord_fname):
try:
coord_f = open(coord_fname, 'U')
except (TypeError, IOError):
raise MissingFileError('Coord file required for this analysis')
coord_header, coords, eigvals, pct_var = parse_coords(coord_f)
return [coord_header, coords, eigvals, pct_var, None, None]
else:
master_pcoa, support_pcoas = load_pcoa_files(coord_fname)
# get Summary statistics
coords, coords_low, coords_high, eigval_average, coord_header = \
summarize_pcoas(master_pcoa, support_pcoas, method=method)
pct_var = master_pcoa[3] # should be getting this from an average
# make_3d_plots expects coord_header to be a python list
coord_header = list(master_pcoa[0])
return (
[coord_header,
coords,
eigval_average,
pct_var,
coords_low,
coords_high]
)
def get_coord(coord_fname, method="IQR"):
"""Opens and returns coords location matrix and metadata.
Also two spread matrices (+/-) if passed a dir of coord files.
If only a single coord file, spread matrices are returned as None.
"""
if not os.path.isdir(coord_fname):
try:
coord_f = open(coord_fname, 'U').readlines()
except (TypeError, IOError):
raise MissingFileError, 'Coord file required for this analysis'
coord_header, coords, eigvals, pct_var = parse_coords(coord_f)
return [coord_header, coords, eigvals, pct_var, None, None]
else:
master_pcoa, support_pcoas = load_pcoa_files(coord_fname)
# get Summary statistics
coords, coords_low, coords_high, eigval_average, coord_header = \
summarize_pcoas(master_pcoa,support_pcoas, method=method)
pct_var = master_pcoa[3] # should be getting this from an average
# make_3d_plots expects coord_header to be a python list
coord_header = list(master_pcoa[0])
return [
coord_header, coords, eigval_average, pct_var, coords_low,
coords_high
]
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
prefs,data,background_color,label_color,ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
data['ellipsoid_method'] = opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data['alpha'] = opts.ellipsoid_opacity
else:
raise ValueError, 'The opacity must be a value between 0 and 1!'
#Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data['coord'], data['support_pcoas'] = load_pcoa_files(
opts.coord_fname)
data['coord'] = get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data['coord'], data['support_pcoas'] = load_pcoa_files(
opts.coord_fname)
else:
data['coord'] = get_coord(opts.coord_fname)
filepath = opts.coord_fname
basename, extension = os.path.splitext(filepath)
filename = '%s_2D_PCoA_plots' % (basename)
qiime_dir = get_qiime_project_dir()
js_path = os.path.join(qiime_dir, 'qiime', 'support_files', 'js')
if opts.output_dir:
if os.path.exists(opts.output_dir):
dir_path = opts.output_dir
else:
try:
os.mkdir(opts.output_dir)
dir_path = opts.output_dir
except OSError:
pass
else:
dir_path = './'
html_dir_path = dir_path
data_dir_path = get_random_directory_name(output_dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path, 'js')
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path,'overlib.js'), \
os.path.join(js_dir_path,'overlib.js'))
try:
action = generate_2d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs, data, html_dir_path, data_dir_path, filename,
background_color, label_color, opts.scree)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
matplotlib_version = re.split("[^\d]", matplotlib.__version__)
matplotlib_version_info = tuple([int(i) for i in matplotlib_version if \
i.isdigit()])
if matplotlib_version_info != (1,1,0):
print "This code was only tested with Matplotlib-1.1.0"
data = {}
prefs,data,background_color,label_color,ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
data['ellipsoid_method']=opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data['alpha']=opts.ellipsoid_opacity
else:
raise ValueError, 'The opacity must be a value between 0 and 1!'
#Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data['coord'],data['support_pcoas'] = load_pcoa_files(opts.coord_fname)
data['coord']=get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data['coord'],data['support_pcoas'] = load_pcoa_files(opts.coord_fname)
else:
data['coord'] = get_coord(opts.coord_fname)
filepath=opts.coord_fname
basename,extension=os.path.splitext(filepath)
filename='%s_2D_PCoA_plots' % (basename)
qiime_dir=get_qiime_project_dir()
js_path=os.path.join(qiime_dir,'qiime','support_files','js')
if opts.output_dir:
if os.path.exists(opts.output_dir):
dir_path=opts.output_dir
else:
try:
os.mkdir(opts.output_dir)
dir_path=opts.output_dir
except OSError:
pass
else:
dir_path='./'
html_dir_path=dir_path
data_dir_path = get_random_directory_name(output_dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path,'js')
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path,'overlib.js'), \
os.path.join(js_dir_path,'overlib.js'))
try:
action = generate_2d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs,data,html_dir_path,data_dir_path,filename,background_color,
label_color,opts.scree)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
prefs, data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
data["ellipsoid_method"] = opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data["alpha"] = opts.ellipsoid_opacity
else:
raise ValueError("The opacity must be a value between 0 and 1!")
# Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data["coord"], data["support_pcoas"] = load_pcoa_files(opts.coord_fname)
data["coord"] = get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data["coord"], data["support_pcoas"] = load_pcoa_files(opts.coord_fname)
else:
data["coord"] = get_coord(opts.coord_fname)
filepath = opts.coord_fname
basename, extension = os.path.splitext(filepath)
filename = "%s_2D_PCoA_plots" % (basename)
# obtaining where the files live so they can be copied
qiime_dir = get_qiime_project_dir()
js_path = os.path.join(qiime_dir, "qiime", "support_files", "js")
if opts.output_dir:
if os.path.exists(opts.output_dir):
dir_path = opts.output_dir
else:
try:
os.mkdir(opts.output_dir)
dir_path = opts.output_dir
except OSError:
pass
else:
dir_path = "./"
html_dir_path = dir_path
data_dir_path = mkdtemp(dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path, "js")
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path, "overlib.js"), os.path.join(js_dir_path, "overlib.js"))
try:
action = generate_2d_plots
except NameError:
action = None
# Place this outside try/except so we don't mask NameError in action
if action:
action(
prefs,
data,
html_dir_path,
data_dir_path,
filename,
background_color,
label_color,
opts.scree,
opts.pct_variation_below_one,
)
