def __init__(self, ini_main, **kws):
self.go2obj = ini_main.go2obj
self.kws = get_kwargs(kws, self.exp_keys, None)
if 'rcntobj' not in kws:
self.kws['rcntobj'] = True
self.kw_elems = self._init_kwelems()
self.relationships = ini_main.relationships
self.prt_flds = self._init_prt_flds()
def _init_kws(self, **kws_usr):
"""Return a dict containing user-specified plotting options."""
kws_self = {}
user_keys = set(kws_usr)
for objname, expset in self.exp_keys.items():
usrkeys_curr = user_keys.intersection(expset)
kws_self[objname] = get_kwargs(kws_usr, usrkeys_curr, usrkeys_curr)
dpi = str(kws_self['dag'].get('dpi', self.dflts['dpi']))
kws_self['dag']['dpi'] = dpi
return kws_self
def __init__(self, gosubdag, objgoea=None, **kws):
# kws: go2color go2bordercolor dflt_bordercolor
self.kws = get_kwargs(kws, self.kws_dct, None)
# Use default key coloring if user does not specify to turn it off (key2col=False)
if 'key2col' not in kws or kws['key2col']:
self.kws['key2col'] = self.key2col
self.gosubdag = gosubdag # GoSubDag
self.objgoea = objgoea # GoeaResults
self.dflt_bordercolor = kws.get('dflt_bordercolor', 'mediumseagreen')
self.go2color = self.init_goid2color()
self.go2bordercolor = kws.get('go2bordercolor', {})
self._init_equiv()
def __init__(self, gosubdag, objgoea=None, **kws):
# kws: go2color go2bordercolor dflt_bordercolor
self.kws = get_kwargs(kws, self.kws_dct, None)
# Use default key coloring if user does not specify to turn it off (key2col=False)
if 'key2col' not in kws or kws['key2col']:
self.kws['key2col'] = self.key2col
self.gosubdag = gosubdag # GoSubDag
self.objgoea = objgoea # GoeaResults
self.dflt_bordercolor = kws.get('dflt_bordercolor', 'mediumseagreen')
self.go2color = self.init_goid2color()
self.go2bordercolor = kws.get('go2bordercolor', {})
self._init_equiv()
def _init_kws(self, **kws_usr):
"""Return a dict containing user-specified plotting options."""
kws_self = {}
user_keys = set(kws_usr)
for objname, expset in self.exp_keys.items():
usrkeys_curr = user_keys.intersection(expset)
kws_self[objname] = get_kwargs(kws_usr, usrkeys_curr, usrkeys_curr)
if 'title' in kws_usr:
kws_self['dag']['label'] = kws_usr['title']
kws_self['dag']['labelloc'] = 't'
if 'go2txt' in kws_usr:
self._init_go2txt_altgos(kws_self['node_go']['go2txt'])
dpi = str(kws_self['dag'].get('dpi', self.dflts['dpi']))
kws_self['dag']['dpi'] = dpi
return kws_self
def _get_docargs(self, args_user, prt):
"""Pare down docopt. Return a minimal dictionary and a set containing runtime arg values."""
if prt is not None:
print("DocOptParse BEFORE docopt: {}".format(args_user))
docargs = docopt(self.doc, args_user)
if prt is not None:
print("DocOptParse AFTER docopt: {}".format(docargs))
kwargs_doc = {re.sub(r'^-{1,2}', '', k): v for k, v in docargs.items()}
self._chk_docopt_kws(kwargs_doc, args_user)
kwargs_usr = get_kwargs(kwargs_doc, self.exp_keys, self.exp_elems)
if prt is not None:
print("DocOptParse AFTER pared: {}".format(kwargs_usr))
for key in ['taxid']:
if key in kwargs_usr:
kwargs_usr[key] = int(kwargs_usr[key])
if prt is not None:
print("DocOptParse AFTER edited/checked: {}".format(kwargs_usr))
return kwargs_usr
def _get_docargs(self, args_user, prt):
"""Pare down docopt. Return a minimal dictionary and a set containing runtime arg values."""
if prt is not None:
print("DocOptParse BEFORE docopt: {}".format(args_user))
docargs = docopt(self.doc, args_user)
if prt is not None:
print("DocOptParse AFTER docopt: {}".format(docargs))
kwargs_doc = {re.sub(r'^-{1,2}', '', k):v for k, v in docargs.items()}
self._chk_docopt_kws(kwargs_doc, args_user)
kwargs_usr = get_kwargs(kwargs_doc, self.exp_keys, self.exp_elems)
if prt is not None:
print("DocOptParse AFTER pared: {}".format(kwargs_usr))
for key in ['taxid']:
if key in kwargs_usr:
kwargs_usr[key] = int(kwargs_usr[key])
if prt is not None:
print("DocOptParse AFTER edited/checked: {}".format(kwargs_usr))
return kwargs_usr
