#!/usr/bin/python ############################################################################### # NAME: new_graphics.py # VERSION: 2.0.0b5 (19DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_renumbering.ini') print '-'*80 print 'INFO: Pedigree ID map: %s' % (example.idmap) print '-'*80 print 'INFO: Pedigree ID reverse map: %s' % (example.backmap) print '-'*80 myinbr = pyp_nrm.inbreeding(example) print 'INFO: Coefficients of inbreeding: %s' % (myinbr) pyp_graphics.draw_pedigree(example,gfilename='new_renumbering',gtitle='My Pedigree')
from PyPedal import pyp_network
import networkx
if __name__ == '__main__':
for i in range(1):
print 'Simulating and drawing pedigree %d' % (i)
example = pyp_newclasses.loadPedigree(optionsfile='new_simulate.ini')
print example
#_gfn = 'simulated_pedigree_%d' % ( i )
_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()
width=example.nrm.nrm.shape[0])
#pyp_db.loadPedigreeTable(example)
pyp_db.deleteTable(example)
pyp_db.populatePedigreeTable(example)
coi_by_year = pyp_reports.meanMetricBy(example, metric='fa', byvar='by')
print 'coi_by_year: ', coi_by_year
cby = coi_by_year
del (cby[1900])
pyp_graphics.plot_line_xy(coi_by_year,
gfilename='dog_coi_by_year',
gtitle='',
gxlabel='Birth year',
gylabel='Coefficient of inbreeding')
pyp_graphics.draw_pedigree(example,
gfilename='dog_pedigree',
gtitle='Dog pedigree',
gformat='jpg',
gsize='f')
pyp_graphics.plot_founders_by_year(
example,
gfilename='dog_founders_by_year',
gtitle='Number of founders within each birthyear')
pyp_graphics.plot_founders_pct_by_year(
example,
gfilename='dog_founder_pct',
gtitle='Percentage of founders within each birthyear')
from PyPedal import pyp_graphics
from PyPedal import pyp_newclasses
from PyPedal import pyp_nrm
from PyPedal import pyp_reports
from PyPedal.pyp_utils import pyp_nice_time
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(optionsfile='new_graphics.ini')
# example_inbreeding = pyp_nrm.inbreeding(example)
pyp_graphics.rmuller_spy_matrix_pil(example.nrm.nrm, fname='dog_sparsity.png', cutoff=0.01, do_outline=0, height=example.nrm.nrm.shape[0], width=example.nrm.nrm.shape[0])
pyp_graphics.rmuller_pcolor_matrix_pil(example.nrm.nrm, fname='dog_long_pcolored.png', do_outline=0, height=example.nrm.nrm.shape[0], width=example.nrm.nrm.shape[0])
#pyp_db.loadPedigreeTable(example)
pyp_db.deleteTable(example)
pyp_db.populatePedigreeTable(example)
coi_by_year = pyp_reports.meanMetricBy(example, metric='fa', byvar='by')
print 'coi_by_year: ', coi_by_year
cby = coi_by_year
del(cby[1900])
pyp_graphics.plot_line_xy(coi_by_year, gfilename='dog_coi_by_year',
gtitle='', gxlabel='Birth year', gylabel='Coefficient of inbreeding')
pyp_graphics.draw_pedigree(example, gfilename='dog_pedigree', gtitle='Dog pedigree',gformat='jpg',gsize='f')
pyp_graphics.plot_founders_by_year(example, gfilename='dog_founders_by_year', gtitle='Number of founders within each birthyear')
pyp_graphics.plot_founders_pct_by_year(example, gfilename='dog_founder_pct', gtitle='Percentage of founders within each birthyear')
#coi_by_year
#print ib
#for _e in example.pedigree:
#print _e.name, _e.fa
print example.kw['paper_size']
#print example.backmap
## Use with new_renumbering.ped.
#pyp_reports.pdf3GenPed([56,72], example)
## Use with horse.ped.
#pyp_reports.pdf3GenPed(["Pie's Joseph","Green's Dingo"], example)
#pyp_reports.pdf3GenPed("Green's Dingo", example,reportfile='greens_dingo_pedigree.pdf')
#pyp_reports.pdf3GenPed(example.namemap.keys(), example)
pyp_graphics.draw_pedigree(example, gfilename='greens_dingo_pedigree', \
gtitle="Green's Dingo pedigree", gname=1, gformat='ps', garrow=1)
#matings = {}
#for s in example.metadata.unique_sire_list:
# for d in example.metadata.unique_dam_list:
# matings[example.pedigree[s-1].name] = example.pedigree[d-1].name
#pyp_metrics.mating_coi_group(matings,example,names=1)
pg = pyp_network.ped_to_graph(example)
#print pg, pg.degree(), pg.nodes()
census = pyp_network.dyad_census(pg, debug=1)
print 'max dyads:\t', ((pg.order() * (pg.order() - 1)) / 2)
print 'census:\t\t', census
#!/usr/bin/python ############################################################################### # NAME: new_graphics2.py # VERSION: 2.0.0b10 (27APRIL2006) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_demog from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_metrics from PyPedal.pyp_utils import pyp_nice_time #import pyp_demog, pyp_graphics, pyp_newclasses, pyp_nrm, pyp_metrics #from pyp_utils import pyp_nice_time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) example = pyp_newclasses.loadPedigree(optionsfile='new_graphics.ini') if example.kw['messages'] == 'verbose': print '[INFO]: Calling pyp_graphics.draw_pedigree() at %s' % (pyp_nice_time()) pyp_graphics.draw_pedigree(example, gfilename='graphics2', gtitle='graphics2 pedigree', gorient='p')
from PyPedal import pyp_newclasses
from PyPedal.pyp_utils import pyp_nice_time
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(optionsfile='new_doug.ini')
if example.kw['messages'] == 'verbose':
print '[INFO]: Calling pyp_graphics.draw_pedigree() at %s' % (
pyp_nice_time())
pyp_graphics.draw_pedigree(example,
gfilename='doug_below',
gtitle='Doug the German Shepherd (B)',
gorient='p',
gname=1,
gdirec='',
gfontsize=12,
garrow=0,
gtitloc='b')
pyp_graphics.draw_pedigree(example,
gfilename='doug_above',
gtitle='Doug the German Shepherd (A)',
gorient='p',
gname=1,
gdirec='',
gfontsize=12,
garrow=0,
gtitloc='t')
#!/usr/bin/python ############################################################################### # NAME: new_graphics2.py # VERSION: 2.0.0b10 (27APRIL2006) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_demog from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_metrics from PyPedal.pyp_utils import pyp_nice_time #import pyp_demog, pyp_graphics, pyp_newclasses, pyp_nrm, pyp_metrics #from pyp_utils import pyp_nice_time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) example = pyp_newclasses.loadPedigree(optionsfile='new_graphics.ini') if example.kw['messages'] == 'verbose': print '[INFO]: Calling pyp_graphics.draw_pedigree() at %s' % ( pyp_nice_time()) pyp_graphics.draw_pedigree(example, gfilename='graphics2', gtitle='graphics2 pedigree', gorient='p')
from PyPedal import pyp_nrm
from PyPedal.pyp_utils import pyp_nice_time
if __name__ == '__main__':
print 'Starting pypedal.py at %s' % (pyp_nice_time())
example = pyp_newclasses.loadPedigree(optionsfile='new_classes.ini')
if example.kw['messages'] == 'verbose':
print '[INFO]: Forming numerator relationship matrix at %s' % (
pyp_nice_time())
my_a = pyp_nrm.fast_a_matrix_r(example.pedigree, example.kw)
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM sparsity at %s' % (pyp_nice_time())
pyp_graphics.rmuller_spy_matrix_pil(my_a, fname='boichard2_spy.png')
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM in pseudocolor at %s' % (
pyp_nice_time())
pyp_graphics.rmuller_pcolor_matrix_pil(my_a, fname='boichard2_pcolor.png')
pyp_graphics.draw_pedigree(example, gfilename='boichard2_pedigree', \
gtitle='', gorient='p', gdirec='RL', gfontsize=12)
print 'Stopping pypedal.py at %s' % (pyp_nice_time())
from PyPedal import pyp_graphics
from PyPedal import pyp_newclasses
from PyPedal import pyp_nrm
from PyPedal.pyp_utils import pyp_nice_time
if __name__ == '__main__':
print 'Starting pypedal.py at %s' % ( pyp_nice_time() )
example = pyp_newclasses.loadPedigree(optionsfile='new_classes.ini')
if example.kw['messages'] == 'verbose':
print '[INFO]: Forming numerator relationship matrix at %s' % ( pyp_nice_time() )
my_a = pyp_nrm.fast_a_matrix_r(example.pedigree,example.kw)
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM sparsity at %s' % ( pyp_nice_time() )
pyp_graphics.rmuller_spy_matrix_pil(my_a,fname='boichard2_spy.png')
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM in pseudocolor at %s' % ( pyp_nice_time() )
pyp_graphics.rmuller_pcolor_matrix_pil(my_a,fname='boichard2_pcolor.png')
pyp_graphics.draw_pedigree(example, gfilename='boichard2_pedigree', \
gtitle='', gorient='p', gdirec='RL', gfontsize=12)
print 'Stopping pypedal.py at %s' % ( pyp_nice_time() )
#!/usr/bin/python ############################################################################### # NAME: new_hartl.py # VERSION: 2.0.0b12 (15MAY2060) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_hartl.ini') pyp_graphics.draw_pedigree( example, gfilename='hartlandclark', gtitle='Pedigree from van Noordwijck and Scharloo (1981)', gorient='p', gname=0, gdirec='', gfontsize=12, garrow=0) example_inbreeding = pyp_nrm.inbreeding(example) print example_inbreeding
from PyPedal import pyp_newclasses
from PyPedal import pyp_graphics
from PyPedal import pyp_network
import networkx
if __name__ == '__main__':
for i in range(1):
print 'Simulating and drawing pedigree %d' % ( i )
example = pyp_newclasses.loadPedigree(optionsfile='new_simulate.ini')
print example
#_gfn = 'simulated_pedigree_%d' % ( i )
_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 )
#coi_by_year
#print ib
#for _e in example.pedigree:
#print _e.name, _e.fa
print example.kw['paper_size']
#print example.backmap
## Use with new_renumbering.ped.
#pyp_reports.pdf3GenPed([56,72], example)
## Use with horse.ped.
#pyp_reports.pdf3GenPed(["Pie's Joseph","Green's Dingo"], example)
#pyp_reports.pdf3GenPed("Green's Dingo", example,reportfile='greens_dingo_pedigree.pdf')
#pyp_reports.pdf3GenPed(example.namemap.keys(), example)
pyp_graphics.draw_pedigree(example, gfilename='greens_dingo_pedigree', \
gtitle="Green's Dingo pedigree", gname=1, gformat='ps', garrow=1)
#matings = {}
#for s in example.metadata.unique_sire_list:
# for d in example.metadata.unique_dam_list:
# matings[example.pedigree[s-1].name] = example.pedigree[d-1].name
#pyp_metrics.mating_coi_group(matings,example,names=1)
pg = pyp_network.ped_to_graph(example)
#print pg, pg.degree(), pg.nodes()
census = pyp_network.dyad_census(pg,debug=1)
print 'max dyads:\t', ( ( pg.order()*(pg.order()-1) ) / 2 )
print 'census:\t\t', census
#!/usr/bin/python ############################################################################### # NAME: new_doug.py # VERSION: 2.0.0b5 (13DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_doug.ini') if example.kw['messages'] == 'verbose': print '[INFO]: Calling pyp_graphics.draw_pedigree() at %s' % (pyp_nice_time()) pyp_graphics.draw_pedigree(example, gfilename='doug_below', gtitle='Doug the German Shepherd (B)', gorient='p', gname=1, gdirec='', gfontsize=12, garrow=0, gtitloc='b') pyp_graphics.draw_pedigree(example, gfilename='doug_above', gtitle='Doug the German Shepherd (A)', gorient='p', gname=1, gdirec='', gfontsize=12, garrow=0, gtitloc='t') pyp_graphics.draw_pedigree(example, gfilename='doug_p_rl_notitle', gtitle='', gorient='p', gname=1, gdirec='RL', gfontsize=12)
#!/usr/bin/python ############################################################################### # NAME: new_hartl.py # VERSION: 2.0.0b12 (15MAY2060) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_hartl.ini') pyp_graphics.draw_pedigree(example, gfilename='hartlandclark', gtitle='Pedigree from van Noordwijck and Scharloo (1981)', gorient='p', gname=0, gdirec='', gfontsize=12, garrow=0) example_inbreeding = pyp_nrm.inbreeding(example) print example_inbreeding