Grid of plots for swp2 thetas
tforest
parent
43f689e764
commit
3f174048f1
125
swp2.py
125
swp2.py
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@ -216,7 +216,7 @@ def plot_k_epochs_thetafolder(folder_path, mu, tgen, breaks = 2, title = "Title"
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plt.title(title)
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plt.savefig(title+'_b'+str(breaks)+'.pdf')
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def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_scale = True):
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def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_scale = True, ax = None):
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#scenari = {}
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cpt = 0
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epochs = {}
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@ -239,15 +239,21 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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mu = mu, relative_theta_scale = theta_scale)
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print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(breaks)+"\n*******\n")
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print(cpt, "theta file(s) have been scanned.")
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my_dpi = 300
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if ax is None:
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# intialize figure
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my_dpi = 300
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plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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plt.xlim(1e-3, 1)
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fnt_size = 18
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fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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else:
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fnt_size = 12
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plt.rcParams['font.size'] = fnt_size
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ax1 = ax[0,0]
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ax1.set_xlim(1e-3, 1)
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#plt.ylim(0, 10)
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plt.yscale('log')
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plt.xscale('log')
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plt.grid(True,which="both", linestyle='--', alpha = 0.3)
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ax1.set_yscale('log')
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ax1.set_xscale('log')
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ax1.grid(True,which="both", linestyle='--', alpha = 0.3)
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brkpt_lik = []
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for epoch, scenari in epochs.items():
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# sort starting by the smallest -log(Likelihood)
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@ -265,22 +271,23 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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# divide by N0
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y[i] = y[i]/N0
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x[i] = x[i]/N0
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plt.plot(x, y, 'o', linestyle = "-", alpha=0.75, lw=2, label = str(epoch)+' BrkPt | Lik='+greatest_likelihood)
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ax1.plot(x, y, 'o', linestyle = "-", alpha=0.75, lw=2, label = str(epoch)+' BrkPt | Lik='+greatest_likelihood)
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if theta_scale:
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plt.xlabel("Coal. time")
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plt.ylabel("Pop. size scaled by N0")
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ax1.set_xlabel("Coal. time")
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ax1.set_ylabel("Pop. size scaled by N0")
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recent_scale_lower_bound = 0.01
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recent_scale_upper_bound = 0.1
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#print(recent_scale_lower_bound, recent_scale_upper_bound)
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plt.axvline(x=recent_scale_lower_bound)
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plt.axvline(x=recent_scale_upper_bound)
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ax1.axvline(x=recent_scale_lower_bound)
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ax1.axvline(x=recent_scale_upper_bound)
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else:
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# years
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plt.xlabel("Time (years)")
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plt.ylabel("Individuals (N)")
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plt.xlim(1e-5, 1)
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plt.legend(loc='upper right')
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plt.title(title)
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plt.set_xlabel("Time (years)")
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plt.set_ylabel("Individuals (N)")
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ax1.set_xlim(1e-5, 1)
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ax1.legend(loc='best', fontsize = fnt_size*0.5)
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ax1.set_title(title)
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if ax is None:
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plt.savefig(title+'_b'+str(breaks)+'.pdf')
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# plot likelihood against nb of breakpoints
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# best possible likelihood from SFS
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@ -299,31 +306,40 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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res = Ln
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# print(res)
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# basic plot likelihood
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plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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if ax is None:
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fig, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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plt.rcParams['font.size'] = '18'
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plt.plot(np.array(brkpt_lik)[:, 0], np.array(brkpt_lik)[:, 1].astype(float), 'o', linestyle = "dotted", lw=2)
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else:
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plt.rcParams['font.size'] = fnt_size
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ax2 = ax[2,0]
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ax2.plot(np.array(brkpt_lik)[:, 0], np.array(brkpt_lik)[:, 1].astype(float), 'o', linestyle = "dotted", lw=2)
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# plt.ylim(0,100)
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# plt.axhline(y=res)
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plt.yscale('log')
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plt.xlabel("# breakpoints", fontsize=20)
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plt.ylabel("$-\log\mathcal{L}$")
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#plt.legend(loc='upper right')
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plt.title(title)
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ax2.axhline(y=-Ln)
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ax2.set_yscale('log')
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ax2.set_xlabel("# breakpoints", fontsize=fnt_size)
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ax2.set_ylabel("$-\log\mathcal{L}$")
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#ax2.legend(loc='best', fontsize = fnt_size*0.5)
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ax2.set_title(title)
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if ax is None:
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plt.savefig(title+'_Breakpts_Likelihood.pdf')
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# AIC
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plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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if ax is None:
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fig, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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plt.rcParams['font.size'] = '18'
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else:
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ax3 = ax[2,1]
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AIC = 2*(len(brkpt_lik)+1)+2*np.array(brkpt_lik)[:, 1].astype(float)
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plt.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
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# plt.axhline(y=106)
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plt.yscale('log')
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plt.xlabel("# breakpoints", fontsize=20)
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plt.ylabel("AIC")
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#plt.legend(loc='upper right')
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plt.title(title)
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ax3.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
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ax3.axhline(y=2*(len(brkpt_lik)+1)-2*Ln)
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ax3.set_yscale('log')
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ax3.set_xlabel("# breakpoints", fontsize=fnt_size)
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ax3.set_ylabel("AIC")
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#ax3.legend(loc='best', fontsize = fnt_size*0.5)
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ax3.set_title(title)
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if ax is None:
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plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')
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def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 12, ax = None):
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return ax
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def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 10, ax = None):
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"""
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Use theta values as is to do basic plots.
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"""
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@ -341,15 +357,16 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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epochs[k] = thetas
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print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(k)+"\n*******\n")
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print(cpt, "theta file(s) have been scanned.")
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# intialize figure 1
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my_dpi = 300
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# plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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# multiple fig
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if ax is None:
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# intialize figure 1
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my_dpi = 300
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fnt_size = 18
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fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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# Add some extra space for the second axis at the bottom
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fig.subplots_adjust(bottom=0.15)
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else:
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fnt_size = 12
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ax1 = ax[0, 1]
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plt.subplots_adjust(wspace=0.3, hspace=0.3)
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@ -389,14 +406,19 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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twin.xaxis.set_ticks_position("bottom")
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twin.xaxis.set_label_position("bottom")
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# Offset the twin axis below the host
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if ax is None:
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# arrange differently the second x axis if the plot is plain
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twin.spines["bottom"].set_position(("axes", -0.15))
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else:
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# in a combined plot, more space between the fig and the axis
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twin.spines["bottom"].set_position(("axes", -0.35))
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#ax.legend(handles=[p0]+plots)
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ax1.set_xlabel("# breaks")
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# Set the x-axis locator to reduce the number of ticks to 10
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ax1.xaxis.set_major_locator(MaxNLocator(nbins=10))
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ax1.set_ylabel("theta")
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# twin.set_ylabel("Proportion")
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plt.legend(handles=plots, loc='upper right')
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twin.set_ylabel("Proportion")
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ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5)
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if ax is None:
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plt.savefig(title+'_raw'+str(k)+'.pdf')
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# fig 2 & 3
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@ -439,43 +461,30 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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ax2.set_xlabel("# breaks")
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ax2.set_ylabel("theta")
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ax2.set_title("Test")
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ax2.legend(handles=lines_fig2, loc='upper right')
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ax2.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5)
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if ax is None:
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plt.savefig(title+'_plot2_'+str(k)+'.pdf')
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ax3.set_xscale('log')
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ax3.set_xlabel("log()")
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ax3.set_ylabel("theta")
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ax3.set_title("Test")
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ax3.legend(handles=lines_fig3, loc='upper right')
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ax3.legend(handles=lines_fig3, loc='best', fontsize = fnt_size*0.5)
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if ax is None:
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plt.savefig(title+'_plot3_'+str(k)+'_log.pdf')
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# return plots
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return ax
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def save_combined_pdf(output_path):
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with PdfPages(output_path) as pdf:
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pdf.savefig()
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def save_multi_image(filename):
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pp = PdfPages(filename)
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fig_nums = plt.get_fignums()
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figs = [plt.figure(n) for n in fig_nums]
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for fig in figs:
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fig.savefig(pp, format='pdf')
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pp.close()
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def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True):
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# plot1, plot2, plot3 = plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale)
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my_dpi = 300
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# Add some extra space for the second axis at the bottom
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fig, axs = plt.subplots(2, 2, figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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fig, axs = plt.subplots(3, 2, figsize=(4500/my_dpi, 2970/my_dpi), dpi=my_dpi)
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ax = plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = axs)
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ax = plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = axs)
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# Adjust layout to prevent clipping of titles
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plt.tight_layout()
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# Adjust absolute space between the top and bottom rows
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plt.subplots_adjust(hspace=0.35) # Adjust this value based on your requirement
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plt.subplots_adjust(hspace=0.7) # Adjust this value based on your requirement
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# Save the entire grid as a single figure
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plt.savefig(title+'_combined.pdf')
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