geinf/swp2.py

import matplotlib.pyplot as plt
import os
import numpy as np
import math
from scipy.special import gammaln
from matplotlib.backends.backend_pdf import PdfPages

def log_facto(k):
    k = int(k)
    if k > 1e6:
        return k * np.log(k) - k + np.log(2*math.pi*k)/2
    val = 0
    for i in range(2, k+1):
        val += np.log(i)
    return val

def log_facto_1(k):
    startf = 1 # start of factorial sequence
    stopf  = int(k+1) # end of of factorial sequence

    q = gammaln(range(startf+1, stopf+1)) # n! = G(n+1)

    return q[-1]

def return_x_y_from_stwp_theta_file(stwp_theta_file, breaks, mu, tgen, relative_theta_scale = False):
    with open(stwp_theta_file, "r") as swp_file:
        # Read the first line
        line = swp_file.readline()
        L = float(line.split()[2])
        rands = swp_file.readline()
        line = swp_file.readline()
        # skip empty lines before SFS
        while line == "\n":
            line = swp_file.readline()
        sfs = np.array(line.split()).astype(float)
        # Process lines until the end of the file
        while line:
            # check at each line
            if line.startswith("dim") :
                dim = int(line.split()[1])
                if dim == breaks+1:
                    likelihood = line.split()[5]
                    groups = line.split()[6:6+dim]
                    theta_site = line.split()[6+dim:6+dim+1+dim]
                elif dim < breaks+1:
                    line = swp_file.readline()
                    continue
                elif dim > breaks+1:
                    break
                    #return 0,0,0
            # Read the next line
            line = swp_file.readline()
    #### END of parsing
    # quit this file if the number of dimensions is incorrect
    if dim < breaks+1:
        return 0,0,0,0,0
    # get n, the last bin of the last group
    # revert the list of groups as the most recent times correspond
    # to the closest and last leafs of the coal. tree.
    groups = groups[::-1]
    theta_site = theta_site[::-1]
    # initiate the dict of times
    t = {}
    # list of thetas
    theta_L = []
    sum_t = 0
    for group_nb, group in enumerate(groups):
        ###print(group_nb, group, theta_site[group_nb], len(theta_site))
        # store all the thetas one by one, with one theta per group
        theta_L.append(float(theta_site[group_nb]))
        # if the group is of size 1
        if len(group.split(',')) == 1:
            i = int(group)
        # if the group size is >1, take the first elem of the group
        # i is the first bin of each group, straight after a breakpoint
        else:
            i = int(group.split(",")[0])
            j = int(group.split(",")[-1])
        t[i] = 0
        #t =
        if len(group.split(',')) == 1:
            k = i
            if relative_theta_scale:
                t[i] += ((theta_L[group_nb] ) / (k*(k-1)))
            else:
                t[i] += ((theta_L[group_nb] ) / (k*(k-1)) * tgen) / mu
        else:
            for k in range(j, i-1, -1 ):
                if relative_theta_scale:
                    t[i] += ((theta_L[group_nb] ) / (k*(k-1)))
                else:
                    t[i] += ((theta_L[group_nb] ) / (k*(k-1)) * tgen) / mu
        # we add the cumulative times at the end
        t[i] += sum_t
        sum_t = t[i]
    # build the y axis (sizes)
    y = []
    for theta in theta_L:
        if relative_theta_scale:
            size = theta
        else:
            # with size N = theta/4mu
            size = theta / (4*mu)
        y.append(size)
        y.append(size)
    # build the time x axis
    x = [0]
    for time in range(0, len(t.values())-1):
        x.append(list(t.values())[time])
        x.append(list(t.values())[time])
    x.append(list(t.values())[len(t.values())-1])
    # if relative_theta_scale:
    #     # rescale
    #     #N0 = y[0]
    #     # for i in range(len(y)):
    #     #     # divide by N0
    #     #     y[i] = y[i]/N0
    #     #     x[i] = x[i]/N0
    return x,y,likelihood,sfs,L

def return_x_y_from_stwp_theta_file_as_is(stwp_theta_file, breaks, mu, tgen, relative_theta_scale = False):
    with open(stwp_theta_file, "r") as swp_file:
        # Read the first line
        line = swp_file.readline()
        L = float(line.split()[2])
        rands = swp_file.readline()
        line = swp_file.readline()
        # skip empty lines before SFS
        while line == "\n":
            line = swp_file.readline()
        sfs = np.array(line.split()).astype(float)
        # Process lines until the end of the file
        while line:
            # check at each line
            if line.startswith("dim") :
                dim = int(line.split()[1])
                if dim == breaks+1:
                    likelihood = line.split()[5]
                    groups = line.split()[6:6+dim]
                    theta_site = line.split()[6+dim:6+dim+1+dim]
                elif dim < breaks+1:
                    line = swp_file.readline()
                    continue
                elif dim > breaks+1:
                    break
                    #return 0,0,0
            # Read the next line
            line = swp_file.readline()
    #### END of parsing
    # quit this file if the number of dimensions is incorrect
    if dim < breaks+1:
        return 0,0
    # get n, the last bin of the last group
    # revert the list of groups as the most recent times correspond
    # to the closest and last leafs of the coal. tree.
    groups = groups[::-1]
    theta_site = theta_site[::-1]

    thetas = {}

    for i in range(len(groups)):
        groups[i] = groups[i].split(',')
        #print(groups[i], len(groups[i]))
        thetas[i] = [float(theta_site[i]), groups[i], likelihood]
    return thetas, sfs

def plot_k_epochs_thetafolder(folder_path, mu, tgen, breaks = 2, title = "Title", theta_scale = True):
    scenari = {}
    cpt = 0
    for file_name in os.listdir(folder_path):
        if os.path.isfile(os.path.join(folder_path, file_name)):
            # Perform actions on each file
            x,y,likelihood,sfs,L = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks,
                                                             tgen = tgen,
                                     mu = mu, relative_theta_scale = theta_scale)
            if x == 0 or y == 0:
                continue
            cpt +=1
            scenari[likelihood] = x,y
    print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(breaks)+"\n*******\n")
    print(cpt, "theta file(s) have been scanned.")
    # sort starting by the smallest -log(Likelihood)
    print(scenari)
    best10_scenari = (sorted(list(scenari.keys())))[:10]
    print("10 greatest Likelihoods", best10_scenari)
    greatest_likelihood = best10_scenari[0]
    x, y = scenari[greatest_likelihood]
    my_dpi = 300
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    plt.plot(x, y, 'r-', lw=2, label = 'Lik='+greatest_likelihood)
    plt.xlim(1e-3, 1)
    plt.ylim(0, 10)
    #plt.yscale('log')
    plt.xscale('log')
    plt.grid(True,which="both", linestyle='--', alpha = 0.3)

    for scenario in best10_scenari[1:]:
        x,y = scenari[scenario]
        #print("\n----  Lik:",scenario,"\n\nt=", x,"\n\nN=",y, "\n\n")
        plt.plot(x, y, '--', lw=1, label = 'Lik='+scenario)
    if theta_scale:
        plt.xlabel("Coal. time")
        plt.ylabel("Pop. size scaled by N0")
        recent_scale_lower_bound = y[0] * 0.01
        recent_scale_upper_bound = y[0] * 0.1
        plt.axvline(x=recent_scale_lower_bound)
        plt.axvline(x=recent_scale_upper_bound)
    else:
        # years
        plt.xlabel("Time (years)")
        plt.ylabel("Individuals (N)")
    plt.legend(loc='upper right')
    plt.title(title)
    plt.savefig(title+'_b'+str(breaks)+'.pdf')

def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_scale = True):
    #scenari = {}
    cpt = 0
    epochs = {}
    for file_name in os.listdir(folder_path):
        breaks = 0
        cpt +=1
        if os.path.isfile(os.path.join(folder_path, file_name)):
            x, y, likelihood, sfs, L = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks,
                                                             tgen = tgen,
                                                             mu = mu, relative_theta_scale = theta_scale)
            SFS_stored = sfs
            L_stored = L
            while not (x == 0 and y == 0):
                if breaks not in epochs.keys():
                    epochs[breaks] = {}
                epochs[breaks][likelihood] = x,y
                breaks += 1
                x,y,likelihood,sfs,L = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks,
                                                                 tgen = tgen,
                                                                  mu = mu, relative_theta_scale = theta_scale)
    print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(breaks)+"\n*******\n")
    print(cpt, "theta file(s) have been scanned.")

    # intialize figure
    my_dpi = 300
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    plt.xlim(1e-3, 1)
    #plt.ylim(0, 10)
    plt.yscale('log')
    plt.xscale('log')
    plt.grid(True,which="both", linestyle='--', alpha = 0.3)
    brkpt_lik = []
    for epoch, scenari in epochs.items():
        # sort starting by the smallest -log(Likelihood)
        best10_scenari = (sorted(list(scenari.keys())))[:10]
        greatest_likelihood = best10_scenari[0]
        # store the tuple breakpoints and likelihood for later plot
        brkpt_lik.append((epoch, greatest_likelihood))
        x, y = scenari[greatest_likelihood]
        #without breakpoint
        if epoch == 0:
            # do something with the theta without bp and skip the plotting
            N0 = y[0]
            #continue
        for i in range(len(y)):
            # divide by N0
            y[i] = y[i]/N0
            x[i] = x[i]/N0
        sum_theta_i = 0
        print(epoch, x, y)
        for i in range(2, len(y)-1):
            sum_theta_i=y[i] / (i-1)
        prop = []
        for k in range(2, len(y)-1):
            prop.append(y[k+1] / (k - 1) / sum_theta_i)
        #print(epoch, prop)
        plt.plot(x, y, 'o', linestyle = "-", alpha=0.75, lw=2, label = str(epoch)+' BrkPt | Lik='+greatest_likelihood)
        if theta_scale:
            plt.xlabel("Coal. time")
            plt.ylabel("Pop. size scaled by N0")
            recent_scale_lower_bound = 0.01
            recent_scale_upper_bound = 0.1
            #print(recent_scale_lower_bound, recent_scale_upper_bound)
            plt.axvline(x=recent_scale_lower_bound)
            plt.axvline(x=recent_scale_upper_bound)
        else:
            # years
            plt.xlabel("Time (years)")
            plt.ylabel("Individuals (N)")
        plt.xlim(1e-5, 1)
        plt.legend(loc='upper right')
        plt.title(title)
        plt.savefig(title+'_b'+str(breaks)+'.pdf')
    # plot likelihood against nb of breakpoints
    # best possible likelihood from SFS
    # Segregating sites
    S = sum(SFS_stored)
    # number of monomorphic sites
    L = L_stored
    S0 = L-S
    print("SFS", SFS_stored)
    print("S", S, "L", L, "S0=", S0)
    # compute Ln
    Ln = log_facto(S+S0) - log_facto(S0) + np.log(float(S0)/(S+S0)) * S0
    for xi in range(0, len(SFS_stored)):
        p_i = SFS_stored[xi] / float(S+S0)
        Ln += np.log(p_i) * SFS_stored[xi] - log_facto(SFS_stored[xi])
    res = Ln
    print(res)
    # basic plot likelihood
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    plt.rcParams['font.size'] = '18'
    plt.plot(np.array(brkpt_lik)[:, 0], np.array(brkpt_lik)[:, 1].astype(float), 'o', linestyle = "dotted", lw=2)
    # plt.ylim(0,100)
    # plt.axhline(y=res)
    plt.yscale('log')
    plt.xlabel("# breakpoints", fontsize=20)
    plt.ylabel("$-\log\mathcal{L}$")
    #plt.legend(loc='upper right')
    plt.title(title)
    plt.savefig(title+'_Breakpts_Likelihood.pdf')
    # AIC
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    plt.rcParams['font.size'] = '18'
    AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 1].astype(float)
    plt.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
    # plt.axhline(y=106)
    plt.yscale('log')
    plt.xlabel("# breakpoints", fontsize=20)
    plt.ylabel("AIC")
    #plt.legend(loc='upper right')
    plt.title(title)
    plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')

def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 5):
    """
    Use theta values as is to do basic plots.
    """
    cpt = 0
    epochs = {}
    for file_name in os.listdir(folder_path):
        cpt +=1
        if os.path.isfile(os.path.join(folder_path, file_name)):
            for k in range(breaks_max):
                thetas,sfs = return_x_y_from_stwp_theta_file_as_is(folder_path+file_name, breaks = k,
                                                                 tgen = tgen,
                                                                 mu = mu, relative_theta_scale = theta_scale)
                if thetas == 0:
                    continue
                epochs[k] = thetas
    print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(k)+"\n*******\n")
    print(cpt, "theta file(s) have been scanned.")

    # intialize figure 1
    my_dpi = 300
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    for epoch, theta in epochs.items():
        groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist()
        x = []
        y = []
        thetas = np.array(list(theta.values()), dtype=object)[:, 0]
        for i,group in enumerate(groups):
            x += group[::-1]
            y += list(np.repeat(thetas[i], len(group)))
            if epoch == 0:
                N0 = y[0]
        for i in range(len(y)):
            y[i] = y[i]/N0
        plt.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks')
        plt.xlabel("# breaks")
        plt.ylabel("theta")
        plt.legend(loc='upper right')
        plt.savefig(title+'_test'+str(k)+'.pdf')
    # fig 2 & 3
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    for epoch, theta in epochs.items():
        groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist()
        x = []
        y = []
        thetas = np.array(list(theta.values()), dtype=object)[:, 0]
        for i,group in enumerate(groups):
            x += group[::-1]
            y += list(np.repeat(thetas[i], len(group)))
            if epoch == 0:
                N0 = y[0]
        for i in range(len(y)):
            y[i] = y[i]/N0
        x_2 = []
        T = 0
        for i in range(len(x)):
            x[i] = int(x[i])
        # compute the times as: theta_k / (k*(k-1))
        for i in range(0, len(x)):
            T += y[i] / (x[i]*(x[i]-1))
            x_2.append(T)
        # Plotting (fig 2)
        plt.plot(x_2, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks')
        plt.xlabel("# breaks")
        plt.ylabel("theta")
        plt.legend(loc='upper right')
        plt.savefig(title+'_test'+str(k)+'.pdf')
        # Plotting (fig 3) which is the same but log scale for x
        plt.plot(x_2, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks')
        plt.xscale('log')
        plt.xlabel("# breaks")
        plt.ylabel("theta")
        plt.legend(loc='upper right')
        plt.savefig(title+'_test'+str(k)+'_log.pdf')

def save_multi_image(filename):
    pp = PdfPages(filename)
    fig_nums = plt.get_fignums()
    figs = [plt.figure(n) for n in fig_nums]
    for fig in figs:
        fig.savefig(pp, format='pdf')
    pp.close()

def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True):
    plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale)
    plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks)
    save_multi_image(title+"_combined.pdf")
if __name__ == "__main__":

    if len(sys.argv) != 4:
        print("Need 3 args: ThetaFolder MutationRate GenerationTime")
        exit(0)

    folder_path = sys.argv[1]
    mu = sys.argv[2]
    tgen = sys.argv[3]

    plot_all_epochs_thetafolder(folder_path, mu, tgen)