'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')