def OnGraphInbreed(self, event):
# try:
if hasattr(self, '_pedigree'):
if not self._pedigree.kw['f_computed']:
_ped_inbr = pyp_nrm.inbreeding(self._pedigree)
pyp_db.loadPedigreeTable(self._pedigree)
_coi_by_year = pyp_reports.meanMetricBy(self._pedigree,
metric='fa',
byvar='by')
del (_coi_by_year[1900])
_graph = pyp_graphics.plot_line_xy(
_coi_by_year,
gfilename='_coi_by_year',
gtitle='Average coefficients of inbreeding',
gxlabel='Birth year',
gylabel='f')
if _graph:
# wx.InitAllImageHandlers()
# _i = wx.Image('_coi_by_year.png', wx.BITMAP_TYPE_PNG)
# _b = wx.BitmapFromImage(_i)
# _sb = wx.StaticBitmap(self, -1, _b, (10, 10), (_b.GetWidth(), _b.GetHeight()))
dlg = pyp_gui_graphs.PyPedalGraphDialogInbreeding(
self, ID_MAIN_TB,
'PyPedal - View inbreeding by birth year')
try:
dlg.ShowModal()
finally:
dlg.Destroy()
def OnGraphInbreed(self,event):
# try:
if hasattr(self,'_pedigree'):
if not self._pedigree.kw['f_computed']:
_ped_inbr = pyp_nrm.inbreeding(self._pedigree)
pyp_db.loadPedigreeTable(self._pedigree)
_coi_by_year = pyp_reports.meanMetricBy(self._pedigree,metric='fa',byvar='by')
del(_coi_by_year[1900])
_graph = pyp_graphics.plot_line_xy(_coi_by_year,gfilename='_coi_by_year',gtitle='Average coefficients of inbreeding',gxlabel='Birth year',gylabel='f')
if _graph:
# wx.InitAllImageHandlers()
# _i = wx.Image('_coi_by_year.png', wx.BITMAP_TYPE_PNG)
# _b = wx.BitmapFromImage(_i)
# _sb = wx.StaticBitmap(self, -1, _b, (10, 10), (_b.GetWidth(), _b.GetHeight()))
dlg = pyp_gui_graphs.PyPedalGraphDialogInbreeding(self,ID_MAIN_TB,'PyPedal - View inbreeding by birth year')
try:
dlg.ShowModal()
finally:
dlg.Destroy()
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')
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')
options['messages'] = 'verbose'
options['pedfile'] = 'hartlandclark.ped'
options['pedname'] = 'Pedigree from van Noordwijck and Scharloo (1981)'
options['pedformat'] = 'asdb'
options['pedigree_is_renumbered'] = 1
options['database_name'] = 'new_db_test'
options['dbtable_name'] = 'test'
options['database_type'] = 'sqlite'
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(options)
pyp_nrm.inbreeding(example)
print 'Dropping existing table...'
pyp_db.deleteTable(example)
print 'Checking to see if the table is gone...'
pyp_db.doesTableExist(example)
print 'Creating the table...'
pyp_db.createPedigreeTable(example)
print 'Populating the table...'
pyp_db.populatePedigreeTable(example)
mean_inbreeding = pyp_reports.meanMetricBy(example,
metric='fa',
byvar='by')
print mean_inbreeding
pyp_graphics.plot_line_xy(mean_inbreeding, gfilename='great_tit_coi_by_year', \
gtitle='', gxlabel='Birth year', gylabel='Coefficient of inbreeding')
options = {}
options['messages'] = 'verbose'
options['pedfile'] = 'hartlandclark.ped'
options['pedname'] = 'Pedigree from van Noordwijck and Scharloo (1981)'
options['pedformat'] = 'asdb'
options['pedigree_is_renumbered'] = 1
options['database_name'] = 'new_db_test'
options['dbtable_name'] = 'test'
options['database_type'] = 'sqlite'
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(options)
pyp_nrm.inbreeding(example)
print 'Dropping existing table...'
pyp_db.deleteTable(example)
print 'Checking to see if the table is gone...'
pyp_db.doesTableExist(example)
print 'Creating the table...'
pyp_db.createPedigreeTable(example)
print 'Populating the table...'
pyp_db.populatePedigreeTable(example)
mean_inbreeding = pyp_reports.meanMetricBy(example,metric='fa',byvar='by')
print mean_inbreeding
pyp_graphics.plot_line_xy(mean_inbreeding, gfilename='great_tit_coi_by_year', \
gtitle='', gxlabel='Birth year', gylabel='Coefficient of inbreeding')