'DOV115b': 'WWD',
'DOV117a': 'WWD',
'DOV117b': 'WWD',
'DOV118a': 'WWD',
'DOV118b': 'WWD',
'DOV119a': 'WWD',
'DOV119b': 'WWD',
'DOV121a': 'WWD',
'DOV121b': 'WWD',
'DOV122a': 'WWD',
'DOV122b': 'WWD'
}
# Generate data dictionary from NeXus alignment
dd = nex_mo.data_dict_from_file('Euro.WWD.nex', pop_assignments)
# Generate frequency spectrum from data dictionary
fs = dadi.Spectrum.from_data_dict(dd, ['Euro', 'WWD'], [18, 18],
polarized=False)
print(fs)
# Print fs to file
fs.tofile('Dove.Euro.WWD.spectra.projection.xx.xx.fs')
# Plot the fs
import pylab
pylab.figure(figsize=(8, 6))
dadi.Plotting.plot_single_2d_sfs(fs, vmin=0.01)
pylab.savefig("Dove.Euro.WWD.sepctra.projection.xx.xx.pdf",
bbox_inches='tight')
'DOV113a':'MD',
'DOV113b':'MD',
'DOV151a':'MD',
'DOV151b':'MD',
'DOV152a':'MD',
'DOV152b':'MD',
'DOV153a':'MD',
'DOV153b':'MD',
'DOV154a':'MD',
'DOV154b':'MD'
}
# Generate data dictionary from NeXus alignment
dd = nex_mo.data_dict_from_file('RP.MD.nex', pop_assignments)
# Generate frequency spectrum from data dictionary
fs = dadi.Spectrum.from_data_dict(dd, ['RP', 'MD'], [20,15], polarized=False)
print (fs)
# Print fs to file
fs.tofile('Dove.RP.MD.spectra.projection.xx.xx.fs')
# Plot the fs
import pylab
pylab.figure(figsize = (8,6))
dadi.Plotting.plot_single_2d_sfs(fs, vmin=0.01)
pylab.savefig("Dove.RP.MD.sepctra.projection.xx.xx.pdf", bbox_inches = 'tight')
pylab.savefig("Dove.RP.MD.sepctra.projection.xx.xx.png", dpi = 300, bbox_inches = 'tight')
'DOV179b': 'RP',
'DOV180a': 'RP',
'DOV180b': 'RP',
'DOV181a': 'RP',
'DOV181b': 'RP',
'DOV182a': 'RP',
'DOV182b': 'RP',
'DOV183a': 'RP',
'DOV183b': 'RP',
'DOV184a': 'RP',
'DOV184b': 'RP',
'DOV185a': 'RP',
'DOV185b': 'RP',
'DOV186a': 'RP',
'DOV186b': 'RP'
}
dd = nex_mo.data_dict_from_file('Dove.RP.nex', pop_assignments)
fs_onepop = dadi.Spectrum.from_data_dict(dd, ['RP'], [28], polarized=False)
import pylab
pylab.figure(figsize=(8, 6))
dadi.Plotting.plot_1d_fs(fs_onepop)
pylab.savefig("Dove.RP.spectra.XX.projection.pdf",
dpi=300,
bbox_inches='tight')
pylab.savefig("Dove.RP.spectra.XX.projection.png",
dpi=300,
bbox_inches='tight')
fs_onepop.tofile('Dove.RP.spectra.XX.projection.fs')