def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#Check the version of Matplotlib
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"
#get QIIME directory
qiime_dir=get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
#get color preferences
color_prefs, color_data, background_color, label_color= \
taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby==None:
colorby=[]
for c in color_data['counts'].values():
colorby.extend(c[0])
else:
colorby=colorby.strip().strip("'").split(',')
counts_fname = opts.counts_fname
#Define labels to use
labels = opts.labels
if not opts.labels:
new_labels=[]
#create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels=','.join(new_labels)
data = [(label,f.strip()) \
for f,label in zip(counts_fname,labels.split(","))]
filepath=data[0][1]
filename=filepath.strip().rpartition('/')[0]
num_categories = int(opts.num_categories)
if num_categories<=0:
raise ValueError, 'The number of categories has to be greater than 0!'
#create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
#make javascript output directory
javascript_path = os.path.join(dir_path,'js')
try:
create_dir(javascript_path)
except OSError: #raised if dir exists
pass
#make raw_data output directory
raw_data_path = os.path.join(dir_path,'raw_data')
try:
create_dir(raw_data_path)
except OSError: #raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'js/overlib.js'),\
os.path.join(javascript_path,'overlib.js'))
#make css output directory
css_path = os.path.join(dir_path,'css')
try:
create_dir(css_path)
except OSError: #raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'css/qiime_style.css'),\
os.path.join(css_path,'qiime_style.css'))
# verify all parameters are valid
plot_width=float(opts.x_width)
if plot_width<=0:
raise ValueError, 'The width of the plot has to be greater than 0!'
plot_height=float(opts.y_height)
if plot_height<=0:
raise ValueError, 'The height of the plot has to be greater than 0!'
bar_width=float(opts.bar_width)
if bar_width<=0 or bar_width>1:
raise ValueError, 'The bar width of the plot has to be between 0 and 1!'
dpi=float(opts.dpi)
if dpi<=0:
raise ValueError, 'The dpi of the plot has to be greater than 0!'
resize_nth_label=int(opts.resize_nth_label)
if resize_nth_label<0:
raise ValueError, 'The resize_nth_label of the plot has to be greater than 0!'
generate_image_type=opts.type_of_file
label_type=opts.label_type
include_html_legend=opts.include_html_legend
include_html_counts=opts.include_html_counts
plots_to_make=opts.chart_type.split(',')
chart_types=['area','pie','bar']
for i in plots_to_make:
chart_type=i.lower().strip()
if chart_type not in chart_types:
raise ValueError, 'Please type in one of the appropriate chart types (i.e. %s)!' % ','.join(chart_types)
#make pie chart output path
charts_path = os.path.join(dir_path,'charts')
try:
create_dir(charts_path)
except OSError: #raised if dir exists
pass
make_all_charts(data,dir_path,filename,num_categories, \
colorby,args,color_data, color_prefs,background_color,label_color,\
chart_type,generate_image_type,plot_width,plot_height,bar_width,dpi,\
resize_nth_label,label_type,include_html_legend,include_html_counts)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#get QIIME directory
qiime_dir=get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
#get color preferences
color_prefs, color_data, background_color, label_color= \
taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby==None:
colorby=[]
for c in color_data['counts'].values():
colorby.extend(c[0])
else:
colorby=colorby.strip().strip("'").split(',')
counts_fname = opts.counts_fname
#Define labels to use
labels = opts.labels
if not opts.labels:
new_labels=[]
#create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels=','.join(new_labels)
data = [(label,f.strip()) \
for f,label in zip(counts_fname,labels.split(","))]
filepath=data[0][1]
filename=filepath.strip().rpartition('/')[0]
num_categories = int(opts.num_categories)
if num_categories<=0:
raise ValueError, 'The number of categories has to be greater than 0!'
#create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
#make javascript output directory
javascript_path = os.path.join(dir_path,'js')
try:
create_dir(javascript_path)
except OSError: #raised if dir exists
pass
#make raw_data output directory
raw_data_path = os.path.join(dir_path,'raw_data')
try:
create_dir(raw_data_path)
except OSError: #raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'js/overlib.js'),\
os.path.join(javascript_path,'overlib.js'))
#make css output directory
css_path = os.path.join(dir_path,'css')
try:
create_dir(css_path)
except OSError: #raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'css/qiime_style.css'),\
os.path.join(css_path,'qiime_style.css'))
# verify all parameters are valid
plot_width=float(opts.x_width)
if plot_width<=0:
raise ValueError, 'The width of the plot has to be greater than 0!'
plot_height=float(opts.y_height)
if plot_height<=0:
raise ValueError, 'The height of the plot has to be greater than 0!'
bar_width=float(opts.bar_width)
if bar_width<=0 or bar_width>1:
raise ValueError, 'The bar width of the plot has to be between 0 and 1!'
dpi=float(opts.dpi)
if dpi<=0:
raise ValueError, 'The dpi of the plot has to be greater than 0!'
resize_nth_label=int(opts.resize_nth_label)
if resize_nth_label<0:
raise ValueError, 'The resize_nth_label of the plot has to be greater\
than 0!'
generate_image_type=opts.type_of_file
label_type=opts.label_type
include_html_legend=opts.include_html_legend
include_html_counts=opts.include_html_counts
plots_to_make=opts.chart_type
for chart_type in plots_to_make:
#make pie chart output path
charts_path = os.path.join(dir_path,'charts')
try:
create_dir(charts_path)
except OSError: #raised if dir exists
pass
make_all_charts(data,dir_path,filename,num_categories, \
colorby,args,color_data, color_prefs,background_color,label_color,\
chart_type,generate_image_type,plot_width,plot_height,bar_width,dpi,\
resize_nth_label,label_type,include_html_legend,include_html_counts)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# get QIIME directory
qiime_dir = get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
# get color preferences
color_prefs, color_data, background_color, label_color = taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby == None:
colorby = []
for c in color_data["counts"].values():
colorby.extend(c[0])
else:
colorby = colorby.strip().strip("'").split(",")
counts_fname = opts.counts_fname
# Define labels to use
labels = opts.labels
if not opts.labels:
new_labels = []
# create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels = ",".join(new_labels)
data = [(label, f.strip()) for f, label in zip(counts_fname, labels.split(","))]
filepath = data[0][1]
filename = filepath.strip().rpartition("/")[0]
num_categories = int(opts.num_categories)
if num_categories <= 0:
raise ValueError, "The number of categories has to be greater than 0!"
# create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
# make javascript output directory
javascript_path = os.path.join(dir_path, "js")
try:
create_dir(javascript_path)
except OSError: # raised if dir exists
pass
# make raw_data output directory
raw_data_path = os.path.join(dir_path, "raw_data")
try:
create_dir(raw_data_path)
except OSError: # raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(
os.path.join(qiime_dir, "qiime", "support_files", "js/overlib.js"), os.path.join(javascript_path, "overlib.js")
)
# make css output directory
css_path = os.path.join(dir_path, "css")
try:
create_dir(css_path)
except OSError: # raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(
os.path.join(qiime_dir, "qiime", "support_files", "css/qiime_style.css"),
os.path.join(css_path, "qiime_style.css"),
)
# verify all parameters are valid
plot_width = float(opts.x_width)
if plot_width <= 0:
raise ValueError, "The width of the plot has to be greater than 0!"
plot_height = float(opts.y_height)
if plot_height <= 0:
raise ValueError, "The height of the plot has to be greater than 0!"
bar_width = float(opts.bar_width)
if bar_width <= 0 or bar_width > 1:
raise ValueError, "The bar width of the plot has to be between 0 and 1!"
dpi = float(opts.dpi)
if dpi <= 0:
raise ValueError, "The dpi of the plot has to be greater than 0!"
resize_nth_label = int(opts.resize_nth_label)
if resize_nth_label < 0:
raise ValueError, "The resize_nth_label of the plot has to be greater\
than 0!"
generate_image_type = opts.type_of_file
label_type = opts.label_type
include_html_legend = opts.include_html_legend
include_html_counts = opts.include_html_counts
plots_to_make = opts.chart_type
for chart_type in plots_to_make:
# make pie chart output path
charts_path = os.path.join(dir_path, "charts")
try:
create_dir(charts_path)
except OSError: # raised if dir exists
pass
make_all_charts(
data,
dir_path,
filename,
num_categories,
colorby,
args,
color_data,
color_prefs,
background_color,
label_color,
chart_type,
generate_image_type,
plot_width,
plot_height,
bar_width,
dpi,
resize_nth_label,
label_type,
include_html_legend,
include_html_counts,
)
