mpl.rc('font', **{'family': 'serif', 'serif': ['Computer Modern'], 'size': 20}); mpl.rc('text', usetex=True) reload(Simulation) reload(utl) reload(est) s=1; nu0=-1 # if zero is given it sets selection on A site with Minimum Allele Frequency. i.e. 1/F FounderLines=150; numReplicates=4 PopulationSize=1000;L=50000 ModelName='SeasonalSNPs' i = 0; filename = '{}/{}/msms/L{:.0f}K.{:04.0f}.msms'.format(popgen.Utils.simoutpath, ModelName, L / 1000, i) initialNeutralGenerations=10 maxGeneration=10 i=0 fig=plt.figure(figsize=(30,35), dpi=60) for i in range(20): plt.subplot(5,4,i+1) sim = Simulation.Simulation(initialNeutralGenerations=initialNeutralGenerations, s=s, L=L, numReplicates=numReplicates, initialCarrierFreq=nu0, msmsFile=filename, F=FounderLines, maxGeneration=maxGeneration, generationStep=1, N=PopulationSize, experimentID=i, ModelName=ModelName, ignoreInitialNeutralGenerations=not True, foldInitialAFs=False) utl.plotNu(sim,fig=fig,show=False) plt.suptitle('Four simulations window of {:.0f}Kbp (roughly {:.0f} variants)'.format(L/1000 , round(sim.theta*sum(1./np.arange(1,150)),0)//100 *100)) plt.savefig('/home/arya/Dropbox/SeasonalSNPs/notes/simulationModel.png') # plt.show()
import matplotlib as mpl; import popgen.Estimate as est import popgen.TimeSeries.RNN.Utils as utl import popgen.Utils from popgen.Utils import Simulation mpl.rc('font', **{'family': 'serif', 'serif': ['Computer Modern'], 'size': 20}); mpl.rc('text', usetex=True) reload(Simulation) reload(utl) reload(est) s=1; nu0=-1 # if zero is given it sets selection on A site with Minimum Allele Frequency. i.e. 1/F FounderLines=150; numReplicates=4 PopulationSize=1000;L=50000 ModelName='SeasonalSNPs' i = 0; filename = '{}/{}/msms/L{:.0f}K.{:04.0f}.msms'.format(popgen.Utils.simoutpath, ModelName, L / 1000, i) initialNeutralGenerations=10 maxGeneration=10 sim = Simulation.Simulation(initialNeutralGenerations=initialNeutralGenerations, s=s, L=L, numReplicates=numReplicates, initialCarrierFreq=nu0, msmsFile=filename, F=FounderLines, maxGeneration=maxGeneration, generationStep=1, N=PopulationSize, experimentID=i, ModelName=ModelName, ignoreInitialNeutralGenerations=True); utl.plotNu(sim)