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Update on swp2 plots

master
tforest 2023-12-01 17:08:13 +01:00
parent 3f174048f1
commit 2e4aca9951
1 changed files with 76 additions and 41 deletions
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swp2.py
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@ -216,6 +216,18 @@ def plot_k_epochs_thetafolder(folder_path, mu, tgen, breaks = 2, title = "Title"
plt.title(title) plt.title(title)
plt.savefig(title+'_b'+str(breaks)+'.pdf') plt.savefig(title+'_b'+str(breaks)+'.pdf')
def plot_straight_x_y(x,y):
x_1 = [x[0]]
y_1 = []
for i in range(0, len(y)-1):
x_1.append(x[i])
x_1.append(x[i])
y_1.append(y[i])
y_1.append(y[i])
y_1 = y_1+[y[-1],y[-1]]
x_1.append(x[-1])
return x_1, y_1
def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_scale = True, ax = None): def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_scale = True, ax = None):
#scenari = {} #scenari = {}
cpt = 0 cpt = 0
@ -237,6 +249,9 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
x,y,likelihood,sfs,L = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks, x,y,likelihood,sfs,L = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks,
tgen = tgen, tgen = tgen,
mu = mu, relative_theta_scale = theta_scale) mu = mu, relative_theta_scale = theta_scale)
if x == 0:
# last break did not work, then breaks = breaks-1
breaks -= 1
print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(breaks)+"\n*******\n") 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.") print(cpt, "theta file(s) have been scanned.")
my_dpi = 300 my_dpi = 300
@ -249,12 +264,12 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
fnt_size = 12 fnt_size = 12
plt.rcParams['font.size'] = fnt_size plt.rcParams['font.size'] = fnt_size
ax1 = ax[0,0] ax1 = ax[0,0]
ax1.set_xlim(1e-3, 1) #ax1.set_xlim(1e-3, 1)
#plt.ylim(0, 10)
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)
brkpt_lik = [] brkpt_lik = []
top_plots = {}
for epoch, scenari in epochs.items(): for epoch, scenari in epochs.items():
# sort starting by the smallest -log(Likelihood) # sort starting by the smallest -log(Likelihood)
best10_scenari = (sorted(list(scenari.keys())))[:10] best10_scenari = (sorted(list(scenari.keys())))[:10]
@ -271,30 +286,44 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
# divide by N0 # divide by N0
y[i] = y[i]/N0 y[i] = y[i]/N0
x[i] = x[i]/N0 x[i] = x[i]/N0
ax1.plot(x, y, 'o', linestyle = "-", alpha=0.75, lw=2, label = str(epoch)+' BrkPt | Lik='+greatest_likelihood) top_plots[greatest_likelihood] = x,y,epoch
if theta_scale: plots_likelihoods = list(top_plots.keys())
ax1.set_xlabel("Coal. time") for i in range(len(plots_likelihoods)):
ax1.set_ylabel("Pop. size scaled by N0") plots_likelihoods[i] = float(plots_likelihoods[i])
recent_scale_lower_bound = 0.01 best10_plots = sorted(plots_likelihoods)[:10]
recent_scale_upper_bound = 0.1 top_plot_lik = str(best10_plots[0])
#print(recent_scale_lower_bound, recent_scale_upper_bound) plot_handles = []
ax1.axvline(x=recent_scale_lower_bound) p0, = ax1.plot(top_plots[top_plot_lik][0], top_plots[top_plot_lik][1], 'o', linestyle = "-",
ax1.axvline(x=recent_scale_upper_bound) alpha=1, lw=2, label = str(top_plots[top_plot_lik][2])+' epoch | Lik='+top_plot_lik)
else: plot_handles.append(p0)
# years for k, plot_Lk in enumerate(best10_plots[1:]):
plt.set_xlabel("Time (years)") plot_Lk = str(plot_Lk)
plt.set_ylabel("Individuals (N)") p, = ax1.plot(top_plots[plot_Lk][0], top_plots[plot_Lk][1], 'o', linestyle = "--",
alpha=1/(k+1), lw=1.5, label = str(top_plots[plot_Lk][2])+' epoch | Lik='+plot_Lk)
plot_handles.append(p)
if theta_scale:
ax1.set_xlabel("Coal. time")
ax1.set_ylabel("Pop. size scaled by N0")
# recent_scale_lower_bound = 0.01
# recent_scale_upper_bound = 0.1
# ax1.axvline(x=recent_scale_lower_bound)
# ax1.axvline(x=recent_scale_upper_bound)
else:
# years
plt.set_xlabel("Time (years)")
plt.set_ylabel("Individuals (N)")
ax1.set_xlim(1e-5, 1) ax1.set_xlim(1e-5, 1)
ax1.legend(loc='best', fontsize = fnt_size*0.5) ax1.legend(handles = plot_handles, loc='best', fontsize = fnt_size*0.5)
ax1.set_title(title) ax1.set_title(title)
if ax is None: if ax is None:
plt.savefig(title+'_b'+str(breaks)+'.pdf') plt.savefig(title+'_b'+str(breaks)+'.pdf')
# plot likelihood against nb of breakpoints # plot likelihood against nb of breakpoints
# best possible likelihood from SFS # best possible likelihood from SFS
# Segregating sites # Segregating sites
S = sum(SFS_stored) S = sum(SFS_stored)
# number of monomorphic sites # Number of kept sites from which the SFS is computed
L = L_stored L = L_stored
# number of monomorphic sites
S0 = L-S S0 = L-S
# print("SFS", SFS_stored) # print("SFS", SFS_stored)
# print("S", S, "L", L, "S0=", S0) # print("S", S, "L", L, "S0=", S0)
@ -303,8 +332,6 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
for xi in range(0, len(SFS_stored)): for xi in range(0, len(SFS_stored)):
p_i = SFS_stored[xi] / float(S+S0) p_i = SFS_stored[xi] / float(S+S0)
Ln += np.log(p_i) * SFS_stored[xi] - log_facto(SFS_stored[xi]) Ln += np.log(p_i) * SFS_stored[xi] - log_facto(SFS_stored[xi])
res = Ln
# print(res)
# basic plot likelihood # basic plot likelihood
if ax is None: if ax is None:
fig, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) fig, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
@ -313,13 +340,12 @@ 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
ax2 = ax[2,0] ax2 = ax[2,0]
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)
# plt.ylim(0,100) ax2.axhline(y=-Ln, linestyle = "-.", color = "red", label = "$-\log\mathcal{L}$ = "+str(round(-Ln, 2)))
ax2.axhline(y=-Ln)
ax2.set_yscale('log') ax2.set_yscale('log')
ax2.set_xlabel("# breakpoints", fontsize=fnt_size) ax2.set_xlabel("# breakpoints", fontsize=fnt_size)
ax2.set_ylabel("$-\log\mathcal{L}$") ax2.set_ylabel("$-\log\mathcal{L}$")
#ax2.legend(loc='best', fontsize = fnt_size*0.5) ax2.legend(loc='best', fontsize = fnt_size*0.8)
ax2.set_title(title) ax2.set_title(title+" Likelihood gain from # breakpoints")
if ax is None: if ax is None:
plt.savefig(title+'_Breakpts_Likelihood.pdf') plt.savefig(title+'_Breakpts_Likelihood.pdf')
# AIC # AIC
@ -330,12 +356,14 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
ax3 = ax[2,1] ax3 = ax[2,1]
AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 1].astype(float) AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 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)
ax3.axhline(y=2*(len(brkpt_lik)+1)-2*Ln) 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)))
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")
#ax3.legend(loc='best', fontsize = fnt_size*0.5) ax3.legend(loc='best', fontsize = fnt_size*0.8)
ax3.set_title(title) ax3.set_title(title+" AIC")
if ax is None: if ax is None:
plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf') plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')
return ax return ax
@ -396,8 +424,9 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
for i in range(len(y)): for i in range(len(y)):
y[i] = y[i]/N0 y[i] = y[i]/N0
# plot # plot
x_plot, y_plot = plot_straight_x_y(x, y)
#plt.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') #plt.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks')
p, = ax1.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
# add plot to the list of all plots to superimpose # add plot to the list of all plots to superimpose
plots.append(p) plots.append(p)
# virtual line to get the second x axis for proportions # virtual line to get the second x axis for proportions
@ -413,11 +442,13 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
# in a combined plot, more space between the fig and the axis # in a combined plot, more space between the fig and the axis
twin.spines["bottom"].set_position(("axes", -0.35)) twin.spines["bottom"].set_position(("axes", -0.35))
#ax.legend(handles=[p0]+plots) #ax.legend(handles=[p0]+plots)
ax1.set_xlabel("# breaks") ax1.set_xlabel("# bin")
# 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.xaxis.set_major_locator(MaxNLocator(nbins=10)) ax1.xaxis.set_major_locator(MaxNLocator(nbins=10))
twin.xaxis.set_major_locator(MaxNLocator(nbins=10))
ax1.set_ylabel("theta") ax1.set_ylabel("theta")
twin.set_ylabel("Proportion") twin.set_ylabel("Proportion")
ax1.set_title("Title")
ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5) ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5)
if ax is None: if ax is None:
plt.savefig(title+'_raw'+str(k)+'.pdf') plt.savefig(title+'_raw'+str(k)+'.pdf')
@ -453,21 +484,24 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
T += y[i] / (x[i]*(x[i]-1)) T += y[i] / (x[i]*(x[i]-1))
x_2.append(T) x_2.append(T)
# Plotting (fig 2) # Plotting (fig 2)
p2, = ax2.plot(x_2, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') x_2 = [0]+x_2
y = [y[0]]+y
x2_plot, y2_plot = plot_straight_x_y(x_2, y)
p2, = ax2.plot(x2_plot, y2_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
lines_fig2.append(p2) lines_fig2.append(p2)
# Plotting (fig 3) which is the same but log scale for x # Plotting (fig 3) which is the same but log scale for x
p3, = ax3.plot(x_2, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks') p3, = ax3.plot(x2_plot, y2_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
lines_fig3.append(p3) lines_fig3.append(p3)
ax2.set_xlabel("# breaks") ax2.set_xlabel("Relative scale")
ax2.set_ylabel("theta") ax2.set_ylabel("theta")
ax2.set_title("Test") ax2.set_title("Title")
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')
ax3.set_xscale('log') ax3.set_xscale('log')
ax3.set_xlabel("log()") ax3.set_xlabel("log Relative scale")
ax3.set_ylabel("theta") ax3.set_ylabel("theta")
ax3.set_title("Test") ax3.set_title("Title")
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')
@ -477,18 +511,19 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True): def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True):
my_dpi = 300 my_dpi = 300
# Add some extra space for the second axis at the bottom # Add some extra space for the second axis at the bottom
fig, axs = plt.subplots(3, 2, figsize=(4500/my_dpi, 2970/my_dpi), dpi=my_dpi) fig, axs = plt.subplots(3, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi)
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() plt.tight_layout()
# Adjust absolute space between the top and bottom rows # Adjust absolute space between the top and bottom rows
plt.subplots_adjust(hspace=0.7) # Adjust this value based on your requirement 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.close()
# second call for individual plots
plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = None)
plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = None)
if __name__ == "__main__": if __name__ == "__main__":