From 89813468b5fb412b361842b2dd4755022a755ee8 Mon Sep 17 00:00:00 2001 From: tforest Date: Thu, 7 Dec 2023 17:35:39 +0100 Subject: [PATCH] First version of the new layout of combined plots --- swp2.py | 147 ++++++++++++++++++++++++++++++++++---------------------- 1 file changed, 89 insertions(+), 58 deletions(-) diff --git a/swp2.py b/swp2.py index 3a4123a..6c4ac18 100644 --- a/swp2.py +++ b/swp2.py @@ -269,7 +269,7 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc else: fnt_size = 12 # plt.rcParams['font.size'] = fnt_size - ax1 = ax[0,0] + ax1 = ax[1][0,0] ax1.set_yscale('log') ax1.set_xscale('log') ax1.grid(True,which="both", linestyle='--', alpha = 0.3) @@ -346,7 +346,7 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc # plt.rcParams['font.size'] = fnt_size else: #plt.rcParams['font.size'] = fnt_size - ax2 = ax[2,0] + ax2 = ax[0][0,1] ax2.plot(np.array(brkpt_lik)[:, 0], np.array(brkpt_lik)[:, 1].astype(float), 'o', linestyle = "dotted", lw=2) ax2.axhline(y=-Ln, linestyle = "-.", color = "red", label = "$-\log\mathcal{L}$ = "+str(round(-Ln, 2))) ax2.set_yscale('log') @@ -362,12 +362,17 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc # plt.rcParams['font.size'] = '18' else: #plt.rcParams['font.size'] = fnt_size - ax3 = ax[2,1] - AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 1].astype(float) + ax3 = ax[1][0,1] + AIC = [] + for brk in np.array(brkpt_lik)[:, 0]: + brk = int(brk) + AIC.append((2*brk+1)+2*np.array(brkpt_lik)[brk, 1].astype(float)) ax3.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2) - AIC_ln = 2*(len(brkpt_lik)+1)-2*Ln + # AIC = 2*k - 2ln(L) ; where k is the number of parameters, here brks+1 + AIC_ln = 2*(len(brkpt_lik)+1) - 2*Ln ax3.axhline(y=AIC_ln, linestyle = "-.", color = "red", label = "Min. AIC = "+str(round(AIC_ln, 2))) + selected_brks_nb = AIC.index(min(AIC)) ax3.set_yscale('log') ax3.set_xlabel("# breakpoints", fontsize=fnt_size) ax3.set_ylabel("AIC") @@ -377,7 +382,7 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf') print("S", S) # return plots - return ax + return ax[0], ax[1] def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 10, output = None): @@ -482,7 +487,53 @@ def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, json.dump(saved_plots, json_file) return saved_plots -def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 10): +def plot_scaled_theta(plot_lines, prop, title, ax = None, n_ticks = 10): + # fig 2 & 3 + if ax is None: + my_dpi = 300 + fnt_size = 18 + fig2, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) + fig3, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) + else: + # plt.rcParams['font.size'] = fnt_size + fnt_size = 12 + # place of plots on the grid + ax2 = ax[1,0] + ax3 = ax[1,1] + lines_fig2 = [] + lines_fig3 = [] + #plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) + for epoch, plot in enumerate(plot_lines): + x,y=plot + x2_plot, y2_plot = plot_straight_x_y(x,y) + p2, = ax2.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks') + lines_fig2.append(p2) + # Plotting (fig 3) which is the same but log scale for x + p3, = ax3.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks') + lines_fig3.append(p3) + ax2.set_xlabel("Relative scale", fontsize=fnt_size) + ax2.set_ylabel("theta", fontsize=fnt_size) + ax2.set_title(title, fontsize=fnt_size) + ax2.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5) + if ax is None: + # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1) + plt.savefig(title+'_plot2_'+str(len(plot_lines))+'.pdf') + # close fig2 to save memory + plt.close(fig2) + ax3.set_xscale('log') + ax3.set_yscale('log') + ax3.set_xlabel("log Relative scale", fontsize=fnt_size) + ax3.set_ylabel("theta", fontsize=fnt_size) + ax3.set_title(title, fontsize=fnt_size) + ax3.legend(handles=lines_fig3, loc='best', fontsize = fnt_size*0.5) + if ax is None: + # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1) + plt.savefig(title+'_plot3_'+str(len(plot_lines))+'_log.pdf') + # close fig3 to save memory + plt.close(fig3) + return ax + +def plot_raw_stairs(plot_lines, prop, title, ax = None, n_ticks = 10): # multiple fig if ax is None: # intialize figure 1 @@ -493,7 +544,7 @@ def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 1 else: fnt_size = 12 # plt.rcParams['font.size'] = fnt_size - ax1 = ax[0, 1] + ax1 = ax[0, 0] plt.subplots_adjust(wspace=0.3, hspace=0.3) plots = [] @@ -508,10 +559,10 @@ def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 1 # print(x_ticks) #print(prop, "\n", sum(prop)) #ax.legend(handles=[p0]+plots) - ax1.set_xlabel("# bin", fontsize=fnt_size) + ax1.set_xlabel("# bin & cumul. prop. of sites", fontsize=fnt_size) # Set the x-axis locator to reduce the number of ticks to 10 ax1.set_ylabel("theta", fontsize=fnt_size) - ax1.set_title("Title", fontsize=fnt_size) + ax1.set_title(title, fontsize=fnt_size) ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5) ax1.set_xticks(x_ticks) step = len(x_ticks)//(n_ticks-1) @@ -523,42 +574,9 @@ def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 1 ax1.set_xticks(values) ax1.set_xticklabels([f'{values[k]}\n{val:.2f}' for k, val in enumerate(new_prop)], fontsize = fnt_size*0.8) if ax is None: - plt.savefig(title+'_raw'+str(k)+'.pdf') - # fig 2 & 3 - if ax is None: - fig2, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) - fig3, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) - else: - # plt.rcParams['font.size'] = fnt_size - # place of plots on the grid - ax2 = ax[1,0] - ax3 = ax[1,1] - lines_fig2 = [] - lines_fig3 = [] - #plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) - for epoch, plot in enumerate(plot_lines2): - x,y=plot - x2_plot, y2_plot = plot_straight_x_y(x,y) - p2, = ax2.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks') - lines_fig2.append(p2) - # Plotting (fig 3) which is the same but log scale for x - p3, = ax3.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks') - lines_fig3.append(p3) - ax2.set_xlabel("Relative scale", fontsize=fnt_size) - ax2.set_ylabel("theta", fontsize=fnt_size) - ax2.set_title("Title", fontsize=fnt_size) - ax2.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5) - if ax is None: - plt.savefig(title+'_plot2_'+str(k)+'.pdf') - ax3.set_xscale('log') - ax3.set_yscale('log') - ax3.set_xlabel("log Relative scale", fontsize=fnt_size) - ax3.set_ylabel("theta", fontsize=fnt_size) - ax3.set_title("Title", fontsize=fnt_size) - ax3.legend(handles=lines_fig3, loc='best', fontsize = fnt_size*0.5) - if ax is None: - plt.savefig(title+'_plot3_'+str(k)+'_log.pdf') - plt.clf() + # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1) + plt.savefig(title+'_raw'+str(len(plot_lines))+'.pdf') + plt.close(fig) # return plots return ax @@ -642,7 +660,7 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, ax1.set_xlabel("# bin", fontsize=fnt_size) # Set the x-axis locator to reduce the number of ticks to 10 ax1.set_ylabel("theta", fontsize=fnt_size) - ax1.set_title("Title", fontsize=fnt_size) + ax1.set_title(title, fontsize=fnt_size) ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5) ax1.set_xticks(x_ticks) if len(prop) >= 18: @@ -699,7 +717,7 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, lines_fig3.append(p3) ax2.set_xlabel("Relative scale", fontsize=fnt_size) ax2.set_ylabel("theta", fontsize=fnt_size) - ax2.set_title("Title", fontsize=fnt_size) + ax2.set_title(title, fontsize=fnt_size) ax2.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5) if ax is None: plt.savefig(title+'_plot2_'+str(k)+'.pdf') @@ -707,7 +725,7 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, ax3.set_yscale('log') ax3.set_xlabel("log Relative scale", fontsize=fnt_size) ax3.set_ylabel("theta", fontsize=fnt_size) - ax3.set_title("Title", fontsize=fnt_size) + ax3.set_title(title, fontsize=fnt_size) ax3.legend(handles=lines_fig3, loc='best', fontsize = fnt_size*0.5) if ax is None: plt.savefig(title+'_plot3_'+str(k)+'_log.pdf') @@ -724,9 +742,8 @@ def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = # ax = plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = axs) # ax = plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = axs) # # Adjust layout to prevent clipping of titles - # plt.tight_layout() - # # Adjust absolute space between the top and bottom rows - # #plt.subplots_adjust(hspace=0.7) # Adjust this value based on your requirement + # + # # Save the entire grid as a single figure # plt.savefig(title+'_combined.pdf') # plt.clf() @@ -735,17 +752,31 @@ def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = # # plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = None) # # plt.clf() # save_k_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, output = title+"_plotdata.json") - with open(title+"_plotdata.json", 'r') as json_file: loaded_data = json.load(json_file) - + # plot page 1 of summary fig1, ax1 = plt.subplots(2, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi) - # plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = ax1) - ax1 = plot_raw_stairs(plot_lines = loaded_data['raw_stairs'], plot_lines2 = loaded_data['scaled_stairs'], + # fig1.tight_layout() + # Adjust absolute space between the top and bottom rows + fig1.subplots_adjust(hspace=0.35) # Adjust this value based on your requirement + # plot page 2 of summary + fig2, ax2 = plt.subplots(2, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi) + # fig2.tight_layout() + ax1 = plot_raw_stairs(plot_lines = loaded_data['raw_stairs'], prop = loaded_data['prop'], title = title, ax = ax1) - plt.savefig(title+'_raw_scaled.pdf') - fig1.clf() + ax1 = plot_scaled_theta(plot_lines = loaded_data['scaled_stairs'], + prop = loaded_data['prop'], title = title, ax = ax1) + ax1, ax2 = plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = [ax1, ax2]) + fig1.savefig(title+'_combined_p1.pdf') + fig2.savefig(title+'_combined_p2.pdf') + plot_raw_stairs(plot_lines = loaded_data['raw_stairs'], + prop = loaded_data['prop'], title = title, ax = None) + plot_scaled_theta(plot_lines = loaded_data['scaled_stairs'], + prop = loaded_data['prop'], title = title, ax = None) + + plt.close(fig1) + plt.close(fig2) if __name__ == "__main__": if len(sys.argv) != 4: