def color_pedigree(pedobj, metric='descendants', places=2, drawer='new', **kw):
"""
color_pedigree() forms a graph object from a pedigree object and determines the
proportion of animals in a pedigree that are descendants of each animal in the
pedigree. The results will be used to feed draw_colored_pedigree().
"""
_dprop = {}
if metric == 'descendants':
_pedgraph = pyp_network.ped_to_graph(pedobj)
# Walk the pedigree and compute proportion of animals in the pedigree that are
# descended from each animal.
for _p in pedobj.pedigree:
_dcount = pyp_network.find_descendants(_pedgraph, _p.animalID, [])
if len(_dcount) < 1:
_dprop[_p.animalID] = 0.0
else:
_dprop[_p.animalID] = round(
float(len(_dcount)) / float(pedobj.metadata.num_records),
places)
del (_pedgraph)
elif metric == 'sons':
for _p in pedobj.pedigree:
_dprop[_p.animalID] = float(len(_p.sons))
#print _dprop
else:
return 0
if drawer == 'new':
new_draw_colored_pedigree(pedobj, _dprop, **kw)
else:
draw_colored_pedigree(pedobj, _dprop, **kw)
def color_pedigree(pedobj, metric='descendants', places=2, drawer='new', **kw):
"""
color_pedigree() forms a graph object from a pedigree object and determines the
proportion of animals in a pedigree that are descendants of each animal in the
pedigree. The results will be used to feed draw_colored_pedigree().
"""
_dprop = {}
if metric == 'descendants':
_pedgraph = pyp_network.ped_to_graph(pedobj)
# Walk the pedigree and compute proportion of animals in the pedigree that are
# descended from each animal.
for _p in pedobj.pedigree:
_dcount = pyp_network.find_descendants(_pedgraph,_p.animalID,[])
if len(_dcount) < 1:
_dprop[_p.animalID] = 0.0
else:
_dprop[_p.animalID] = round(float(len(_dcount)) / float(pedobj.metadata.num_records), places)
del(_pedgraph)
elif metric == 'sons':
for _p in pedobj.pedigree:
_dprop[_p.animalID] = float(len(_p.sons))
#print _dprop
else:
return 0
if drawer == 'new':
new_draw_colored_pedigree(pedobj, _dprop, **kw)
else:
draw_colored_pedigree(pedobj, _dprop, **kw)
_gfn = 'simulated_pedigree'
_gt = 'Simulated Pedigree %d' % (i)
pyp_graphics.draw_pedigree(example,
gfilename=_gfn,
gtitle=_gt,
gformat='ps',
garrow=0,
gclusters=0)
#print 'Animal\tOriginal\tSire\tDam\tSex\tGen'
#for _p in example.pedigree:
#print '%s\t%s\t\t%s\t%s\t%s\t%s' % ( _p.animalID, _p.originalID, _p.sireID, _p.damID, _p.sex, _p.gen )
#print example.idmap
pg = pyp_network.ped_to_graph(example)
pgd = networkx.is_directed_acyclic_graph(pg)
print 'is_directed_acyclic_graph: %s' % (pgd)
pgu = pg.to_undirected()
pgc = networkx.is_connected(pgu)
print 'is_connected: %s' % (pgc)
pgncc = networkx.number_connected_components(pgu)
print 'number_connected_components: %s' % (pgncc)
ped_deg = pyp_network.get_node_degrees(pg)
ped_hist = pyp_network.get_node_degree_histograms(ped_deg)
print 'ped_hist:\t'
for k, v in ped_hist.iteritems():
from PyPedal.pyp_utils import pyp_nice_time
try:
import networkx
except ImportError:
logging.error('The networkx module could not be imported in pyp_network. Routines using networkx functionality are not available.')
if __name__=='__main__':
print 'Starting pypedal.py at %s' % ( pyp_nice_time() )
print '\tLoading pedigree at %s' % ( pyp_nice_time() )
example = pyp_newclasses.loadPedigree(optionsfile='new_networkx.ini')
print 'Calling pyp_network.ped_to_graph()'
ng = pyp_network.ped_to_graph(example)
# print 'The graph has %d nodes' % len(ng.nodes())
# print ng.nodes()
# print ng.edges()
#
## print 'Drawing graph madeup.ps'
## networkx.drawing.draw(ng)
## networkx.drawing.savefig("madeup.ps")
##
## print 'Drawing graph madeup.dot'
## networkx.drawing.write_dot(ng,path="madeup.dot")
## networkx.drawing.draw_nxpydot(ng)
#
# print 'Number of animals in pedigree: %s' % ( ng.order() )
# print ng.nodes()