diff --git a/swp2.py b/swp2.py index 8c28299..2c3f3e3 100644 --- a/swp2.py +++ b/swp2.py @@ -4,6 +4,7 @@ import numpy as np import math from scipy.special import gammaln from matplotlib.backends.backend_pdf import PdfPages +from matplotlib.ticker import MaxNLocator def log_facto(k): k = int(k) @@ -320,7 +321,7 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc 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): +def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 12): """ Use theta values as is to do basic plots. """ @@ -338,10 +339,17 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, 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) + # plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) + # multiple fig + fig, ax = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) + # Add some extra space for the second axis at the bottom + fig.subplots_adjust(bottom=0.15) + twin = ax.twiny() + # Offset the right spine of twin2 + # twin.spines.right.set_position(("axes", 1.2)) + plots = [] for epoch, theta in epochs.items(): groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist() x = [] @@ -352,21 +360,38 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, y += list(np.repeat(thetas[i], len(group))) if epoch == 0: N0 = y[0] + # compute the proportion of information used at each bin of the SFS + sum_theta_i = 0 + for i in range(2, len(y)+2): + sum_theta_i+=y[i-2] / (i-1) + prop = [] + for k in range(2, len(y)+2): + prop.append(y[k-2] / (k - 1) / sum_theta_i) + prop = prop[::-1] + # print(prop, "\n", sum(prop)) + # normalise to N0 (N0 of epoch1) for i in range(len(y)): y[i] = y[i]/N0 - # compute the proportion of information used at each bin of the SFS - sum_theta_i = 0 - 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] / (k - 1) / sum_theta_i) - # plot - 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') + # plot + #plt.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') + p, = ax.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') + # add plot to the list of all plots to superimpose + plots.append(p) + # virtual line to get the second x axis for proportions + p0, = twin.plot(prop, y, alpha = 0, label="Proportion") + # Move twinned axis ticks and label from top to bottom + twin.xaxis.set_ticks_position("bottom") + twin.xaxis.set_label_position("bottom") + # Offset the twin axis below the host + twin.spines["bottom"].set_position(("axes", -0.1)) + #ax.legend(handles=[p0]+plots) + ax.set_xlabel("# breaks") + # Set the x-axis locator to reduce the number of ticks = 10 + ax.xaxis.set_major_locator(MaxNLocator(nbins=10)) + ax.set_ylabel("theta") + # twin.set_ylabel("Proportion") + plt.legend(handles=plots, loc='upper right') + plt.savefig(title+'_raw'+str(k)+'.pdf') # fig 2 & 3 plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) for epoch, theta in epochs.items(): @@ -394,14 +419,14 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, plt.xlabel("# breaks") plt.ylabel("theta") plt.legend(loc='upper right') - plt.savefig(title+'_test'+str(k)+'.pdf') + plt.savefig(title+'_plot2_'+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') + plt.savefig(title+'_plot3_'+str(k)+'_log.pdf') def save_multi_image(filename): pp = PdfPages(filename)