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First version of the new layout of combined plots

master
tforest 2023-12-07 17:35:39 +01:00
parent eb2799bc98
commit 89813468b5
1 changed files with 89 additions and 58 deletions
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swp2.py
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@ -269,7 +269,7 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
else: else:
fnt_size = 12 fnt_size = 12
# plt.rcParams['font.size'] = fnt_size # plt.rcParams['font.size'] = fnt_size
ax1 = ax[0,0] ax1 = ax[1][0,0]
ax1.set_yscale('log') ax1.set_yscale('log')
ax1.set_xscale('log') ax1.set_xscale('log')
ax1.grid(True,which="both", linestyle='--', alpha = 0.3) 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 # plt.rcParams['font.size'] = fnt_size
else: else:
#plt.rcParams['font.size'] = fnt_size #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.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.axhline(y=-Ln, linestyle = "-.", color = "red", label = "$-\log\mathcal{L}$ = "+str(round(-Ln, 2)))
ax2.set_yscale('log') 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' # plt.rcParams['font.size'] = '18'
else: else:
#plt.rcParams['font.size'] = fnt_size #plt.rcParams['font.size'] = fnt_size
ax3 = ax[2,1] ax3 = ax[1][0,1]
AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 1].astype(float) 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) ax3.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
# AIC = 2*k - 2ln(L) ; where k is the number of parameters, here brks+1
AIC_ln = 2*(len(brkpt_lik)+1) - 2*Ln AIC_ln = 2*(len(brkpt_lik)+1) - 2*Ln
ax3.axhline(y=AIC_ln, linestyle = "-.", color = "red", ax3.axhline(y=AIC_ln, linestyle = "-.", color = "red",
label = "Min. AIC = "+str(round(AIC_ln, 2))) label = "Min. AIC = "+str(round(AIC_ln, 2)))
selected_brks_nb = AIC.index(min(AIC))
ax3.set_yscale('log') ax3.set_yscale('log')
ax3.set_xlabel("# breakpoints", fontsize=fnt_size) ax3.set_xlabel("# breakpoints", fontsize=fnt_size)
ax3.set_ylabel("AIC") 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') plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')
print("S", S) print("S", S)
# return plots # return plots
return ax return ax[0], ax[1]
def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
breaks_max = 10, output = None): 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) json.dump(saved_plots, json_file)
return saved_plots 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 # multiple fig
if ax is None: if ax is None:
# intialize figure 1 # intialize figure 1
@ -493,7 +544,7 @@ def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 1
else: else:
fnt_size = 12 fnt_size = 12
# plt.rcParams['font.size'] = fnt_size # plt.rcParams['font.size'] = fnt_size
ax1 = ax[0, 1] ax1 = ax[0, 0]
plt.subplots_adjust(wspace=0.3, hspace=0.3) plt.subplots_adjust(wspace=0.3, hspace=0.3)
plots = [] plots = []
@ -508,10 +559,10 @@ def plot_raw_stairs(plot_lines, plot_lines2, prop, title, ax = None, n_ticks = 1
# print(x_ticks) # print(x_ticks)
#print(prop, "\n", sum(prop)) #print(prop, "\n", sum(prop))
#ax.legend(handles=[p0]+plots) #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 # Set the x-axis locator to reduce the number of ticks to 10
ax1.set_ylabel("theta", fontsize=fnt_size) 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.legend(handles=plots, loc='best', fontsize = fnt_size*0.5)
ax1.set_xticks(x_ticks) ax1.set_xticks(x_ticks)
step = len(x_ticks)//(n_ticks-1) 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_xticks(values)
ax1.set_xticklabels([f'{values[k]}\n{val:.2f}' for k, val in enumerate(new_prop)], fontsize = fnt_size*0.8) 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: if ax is None:
plt.savefig(title+'_raw'+str(k)+'.pdf') # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1)
# fig 2 & 3 plt.savefig(title+'_raw'+str(len(plot_lines))+'.pdf')
if ax is None: plt.close(fig)
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()
# return plots # return plots
return ax 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) ax1.set_xlabel("# bin", fontsize=fnt_size)
# Set the x-axis locator to reduce the number of ticks to 10 # Set the x-axis locator to reduce the number of ticks to 10
ax1.set_ylabel("theta", fontsize=fnt_size) 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.legend(handles=plots, loc='best', fontsize = fnt_size*0.5)
ax1.set_xticks(x_ticks) ax1.set_xticks(x_ticks)
if len(prop) >= 18: 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) lines_fig3.append(p3)
ax2.set_xlabel("Relative scale", fontsize=fnt_size) ax2.set_xlabel("Relative scale", fontsize=fnt_size)
ax2.set_ylabel("theta", 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) ax2.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5)
if ax is None: if ax is None:
plt.savefig(title+'_plot2_'+str(k)+'.pdf') 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_yscale('log')
ax3.set_xlabel("log Relative scale", fontsize=fnt_size) ax3.set_xlabel("log Relative scale", fontsize=fnt_size)
ax3.set_ylabel("theta", 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) ax3.legend(handles=lines_fig3, loc='best', fontsize = fnt_size*0.5)
if ax is None: if ax is None:
plt.savefig(title+'_plot3_'+str(k)+'_log.pdf') 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_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) # ax = plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = axs)
# # Adjust layout to prevent clipping of titles # # 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 # # Save the entire grid as a single figure
# plt.savefig(title+'_combined.pdf') # plt.savefig(title+'_combined.pdf')
# plt.clf() # 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) # # plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = None)
# # plt.clf() # # plt.clf()
# save_k_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, output = title+"_plotdata.json") # 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: with open(title+"_plotdata.json", 'r') as json_file:
loaded_data = json.load(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) 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) # fig1.tight_layout()
ax1 = plot_raw_stairs(plot_lines = loaded_data['raw_stairs'], plot_lines2 = loaded_data['scaled_stairs'], # 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) prop = loaded_data['prop'], title = title, ax = ax1)
plt.savefig(title+'_raw_scaled.pdf') ax1 = plot_scaled_theta(plot_lines = loaded_data['scaled_stairs'],
fig1.clf() 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 __name__ == "__main__":
if len(sys.argv) != 4: if len(sys.argv) != 4: