def parse_struct_plot_settings(config_parser):
''' Parses custom settings for a structure plot from a configuration file. Returns a dictionary containing
all of the settings
config is a ConfigParser object which already contains all of the settings
data is a pandas.DataFrame object containing all of the alternative splicing data
'''
print 'Parsing settings for structure plot...'
settings = default_struct_settings()
FLOAT_PARAMS = set(['plot_width',
'plot_height',
'left_margin',
'right_margin',
'top_margin',
'bottom_margin',
'axis_thickness',
'tick_length',
'horiz_label_size',
'horiz_label_spacing',
'horiz_axis_title_size',
'horiz_axis_title_spacing',
'vertical_tick_spacing',
'vert_label_size',
'vert_label_spacing',
'key_title_size',
'key_font_size'])
BOOLEAN_PARAMS = set(['draw_struct_plot',
'use_vertical_ticks',
'include_key',
'use_custom_key_labels'])
OTHER_PARAMS = set(['horiz_axis_title',
'colors',
'axis_color',
'output_file_path',
'key_text_color',
'key_position'])
for option in config_parser.options('struct_plot'):
if option in FLOAT_PARAMS:
settings[option] = config_parser.getfloat('struct_plot',option)
elif option in BOOLEAN_PARAMS:
settings[option] = config_parser.getboolean('struct_plot',option)
elif option in OTHER_PARAMS:
settings[option] = ast.literal_eval(config_parser.get('struct_plot',option))
# check to make sure entries in settings have the correct format
if type(settings['colors']) is not list:
print 'colors must be a list of 3 element lists'
sys.exit(1)
else:
colorified = [None] * len(settings['colors'])
try:
for i in range(len(colorified)):
colorified[i] = RGB.from_hex_string(settings['colors'][i])
settings['colors'] = colorified
except Exception:
print 'Invalid colors in colors'
sys.exit(1)
try:
settings['axis_color'] = RGB.from_hex_string(settings['axis_color'])
except Exception:
print 'Invalid color in axis_color'
sys.exit(1)
if settings['include_key']:
try:
settings['key_text_color'] = RGB.from_hex_string(settings['key_text_color'])
except Exception:
print 'Invalid color in key_text_color'
sys.exit(1)
if len(settings['key_position']) != 2:
print 'Invalid number of components in key_position'
sys.exit(1)
for i in range(2):
try:
settings['key_position'][i] = float(settings['key_position'][i])
except Exception:
print 'Elements in key_position must be numbers'
sys.exit(1)
return settings
def parse_struct_plot_settings(config_parser):
''' Parses custom settings for a structure plot from a configuration file. Returns a dictionary containing
all of the settings
config is a ConfigParser object which already contains all of the settings
data is a pandas.DataFrame object containing all of the alternative splicing data
'''
print 'Parsing settings for structure plot...'
settings = default_struct_settings()
FLOAT_PARAMS = set(['plot_width',
'plot_height',
'left_margin',
'right_margin',
'top_margin',
'bottom_margin',
'axis_thickness',
'tick_length',
'horiz_label_size',
'horiz_label_spacing',
'horiz_axis_title_size',
'horiz_axis_title_spacing',
'vertical_tick_spacing',
'vert_label_size',
'vert_label_spacing',
'key_title_size',
'key_font_size'])
BOOLEAN_PARAMS = set(['draw_struct_plot',
'use_vertical_ticks',
'include_key',
'use_custom_key_labels'])
OTHER_PARAMS = set(['horiz_axis_title',
'colors',
'axis_color',
'output_file_path',
'key_text_color',
'key_position'])
for option in config_parser.options('struct_plot'):
if option in FLOAT_PARAMS:
settings[option] = config_parser.getfloat('struct_plot',option)
elif option in BOOLEAN_PARAMS:
settings[option] = config_parser.getboolean('struct_plot',option)
elif option in OTHER_PARAMS:
settings[option] = ast.literal_eval(config_parser.get('struct_plot',option))
# check to make sure entries in settings have the correct format
if type(settings['colors']) is not list:
print 'colors must be a list of 3 element lists'
sys.exit(1)
else:
colorified = [None] * len(settings['colors'])
try:
for i in range(len(colorified)):
colorified[i] = RGB.from_hex_string(settings['colors'][i])
settings['colors'] = colorified
except Exception:
print 'Invalid colors in colors'
sys.exit(1)
try:
settings['axis_color'] = RGB.from_hex_string(settings['axis_color'])
except Exception:
print 'Invalid color in axis_color'
sys.exit(1)
if settings['include_key']:
try:
settings['key_text_color'] = RGB.from_hex_string(settings['key_text_color'])
except Exception:
print 'Invalid color in key_text_color'
sys.exit(1)
if len(settings['key_position']) != 2:
print 'Invalid number of components in key_position'
sys.exit(1)
for i in range(2):
try:
settings['key_position'][i] = float(settings['key_position'][i])
except Exception:
print 'Elements in key_position must be numbers'
sys.exit(1)
return settings
def parse_hive_plot_settings(config):
''' Parses custom settings for a hive plot from a configuration file. Returns a dictionary containing all
of the settings
config is a ConfigParser object which already contains all of the settings
data is a pandas.DataFrame object containing all of the alternative splicing data
'''
print 'Parsing settings for hive plot...'
settings = default_hive_settings()
FLOAT_PARAMS = set(['dimension',
'axis_subdivision',
'tick_label_font_size',
'tick_label_distance',
'axis_start_radius',
'axis_end_radius',
'bezier_thickness',
'axis_thickness',
'tick_height',
'tick_thickness',
'axis_label_size',
'key_font_size',
'key_title_size'])
BOOLEAN_PARAMS = set(['tick_marks',
'tick_labels',
'draw_bars',
'include_key',
'draw_hive_plot'])
OTHER_PARAMS = set(['axis_colors',
'bezier_colors',
'axis_angles',
'custom_scale',
'axis_label_radius',
'key_position',
'key_text_color',
'key_position'])
for option in config.options('hive_plot'):
if option in FLOAT_PARAMS:
settings[option] = config.getfloat('hive_plot',option)
elif option in BOOLEAN_PARAMS:
settings[option] = config.getboolean('hive_plot',option)
elif option in OTHER_PARAMS:
settings[option] = ast.literal_eval(config.get('hive_plot',option))
# check to make sure that the settings have the right format and preprocess them
colorified = [None] * len(settings['bezier_colors'])
try:
for i in range(len(colorified)):
colorified[i] = RGB.from_hex_string(settings['bezier_colors'][i])
settings['bezier_colors'] = colorified
except Exception:
print 'Invalid colors in bezier_colors'
sys.exit(1)
try:
settings['axis_colors'] = RGB.from_hex_string(settings['axis_colors'])
except Exception:
print 'Invalid color in axis_colors'
sys.exit(1)
if settings['custom_scale']:
if type(settings['custom_scale']) is not list:
print 'custom_scale must be list'
sys.exit(1)
for item in settings['custom_scale']:
if type(item) is not list:
print 'Items in custom_scale must be list'
sys.exit(1)
elif len(item) != 2:
print 'Invalid number of elements in element of custom_scale'
sys.exit(1)
elif item[0] < 0 or item[0] > 1 or item[1] < item[0] or item[1] > 1:
print 'Invalid boundary in custom_scale'
sys.exit(1)
if settings['include_key']:
if type(settings['key_position']) is not list:
print 'key_position must be list'
sys.exit(1)
if len(settings['key_position']) != 2:
print 'key_position can have exactly 2 coordinates'
sys.exit(1)
try:
settings['key_text_color'] = RGB.from_hex_string(settings['key_text_color'])
except:
print 'key_text_color is not a valid color'
return settings
def parse_hive_plot_settings(config):
''' Parses custom settings for a hive plot from a configuration file. Returns a dictionary containing all
of the settings
config is a ConfigParser object which already contains all of the settings
data is a pandas.DataFrame object containing all of the alternative splicing data
'''
print 'Parsing settings for hive plot...'
settings = default_hive_settings()
FLOAT_PARAMS = set(['dimension',
'axis_subdivision',
'tick_label_font_size',
'tick_label_distance',
'axis_start_radius',
'axis_end_radius',
'bezier_thickness',
'axis_thickness',
'tick_height',
'tick_thickness',
'axis_label_size',
'key_font_size',
'key_title_size'])
BOOLEAN_PARAMS = set(['tick_marks',
'tick_labels',
'draw_bars',
'include_key',
'draw_hive_plot'])
OTHER_PARAMS = set(['axis_colors',
'bezier_colors',
'axis_angles',
'custom_scale',
'axis_label_radius',
'key_position',
'key_text_color',
'key_position'])
for option in config.options('hive_plot'):
if option in FLOAT_PARAMS:
settings[option] = config.getfloat('hive_plot',option)
elif option in BOOLEAN_PARAMS:
settings[option] = config.getboolean('hive_plot',option)
elif option in OTHER_PARAMS:
settings[option] = ast.literal_eval(config.get('hive_plot',option))
# check to make sure that the settings have the right format and preprocess them
colorified = [None] * len(settings['bezier_colors'])
try:
for i in range(len(colorified)):
colorified[i] = RGB.from_hex_string(settings['bezier_colors'][i])
settings['bezier_colors'] = colorified
except Exception:
print 'Invalid colors in bezier_colors'
sys.exit(1)
try:
settings['axis_colors'] = RGB.from_hex_string(settings['axis_colors'])
except Exception:
print 'Invalid color in axis_colors'
sys.exit(1)
if settings['custom_scale']:
if type(settings['custom_scale']) is not list:
print 'custom_scale must be list'
sys.exit(1)
for item in settings['custom_scale']:
if type(item) is not list:
print 'Items in custom_scale must be list'
sys.exit(1)
elif len(item) != 2:
print 'Invalid number of elements in element of custom_scale'
sys.exit(1)
elif item[0] < 0 or item[0] > 1 or item[1] < item[0] or item[1] > 1:
print 'Invalid boundary in custom_scale'
sys.exit(1)
if settings['include_key']:
if type(settings['key_position']) is not list:
print 'key_position must be list'
sys.exit(1)
if len(settings['key_position']) != 2:
print 'key_position can have exactly 2 coordinates'
sys.exit(1)
try:
settings['key_text_color'] = RGB.from_hex_string(settings['key_text_color'])
except:
print 'key_text_color is not a valid color'
return settings