Fixing plot font size issues

swp2.py

@@ -7,7 +7,7 @@ from matplotlib.backends.backend_pdf import PdfPages
 from matplotlib.ticker import MaxNLocator
 import io
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
-
+from matplotlib.ticker import MultipleLocator
 def log_facto(k):
     k = int(k)
     if k > 1e6:
@@ -259,10 +259,11 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
         # intialize figure
         my_dpi = 300
         fnt_size = 18
+        # plt.rcParams['font.size'] = fnt_size
         fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
     else:
         fnt_size = 12
-        plt.rcParams['font.size'] = fnt_size
+        # plt.rcParams['font.size'] = fnt_size
         ax1 = ax[0,0]
     #ax1.set_xlim(1e-3, 1)
     ax1.set_yscale('log')
@@ -293,26 +294,30 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
     best10_plots = sorted(plots_likelihoods)[:10]
     top_plot_lik = str(best10_plots[0])
     plot_handles = []
+    # plt.rcParams['font.size'] = fnt_size
     p0, = ax1.plot(top_plots[top_plot_lik][0], top_plots[top_plot_lik][1], 'o', linestyle = "-",
-    alpha=1, lw=2, label = str(top_plots[top_plot_lik][2])+' epoch | Lik='+top_plot_lik)
+    alpha=1, lw=2, label = str(top_plots[top_plot_lik][2])+' brks | Lik='+top_plot_lik)
     plot_handles.append(p0)
     for k, plot_Lk in enumerate(best10_plots[1:]):
         plot_Lk = str(plot_Lk)
+        # plt.rcParams['font.size'] = fnt_size
         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)
+        alpha=1/(k+1), lw=1.5, label = str(top_plots[plot_Lk][2])+' brks | Lik='+plot_Lk)
         plot_handles.append(p)
     if theta_scale:
-        ax1.set_xlabel("Coal. time")
-        ax1.set_ylabel("Pop. size scaled by N0")
+        ax1.set_xlabel("Coal. time", fontsize=fnt_size)
+        ax1.set_ylabel("Pop. size scaled by N0", fontsize=fnt_size)
         # 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)")
+        plt.set_xlabel("Time (years)", fontsize=fnt_size)
+        plt.set_ylabel("Individuals (N)", fontsize=fnt_size)
         ax1.set_xlim(1e-5, 1)
+    # plt.rcParams['font.size'] = fnt_size
+    # print(fnt_size, "rcParam font.size=", plt.rcParams['font.size'])
     ax1.legend(handles = plot_handles, loc='best', fontsize = fnt_size*0.5)
     ax1.set_title(title)
     if ax is None:
@@ -335,24 +340,25 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
     # basic plot likelihood
     if ax is None:
         fig, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
-        plt.rcParams['font.size'] = '18'
+        # plt.rcParams['font.size'] = fnt_size
     else:
-        plt.rcParams['font.size'] = fnt_size
+        #plt.rcParams['font.size'] = fnt_size
         ax2 = ax[2,0]
     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')
     ax2.set_xlabel("# breakpoints", fontsize=fnt_size)
-    ax2.set_ylabel("$-\log\mathcal{L}$")
-    ax2.legend(loc='best', fontsize = fnt_size*0.8)
+    ax2.set_ylabel("$-\log\mathcal{L}$", fontsize=fnt_size)
+    ax2.legend(loc='best', fontsize = fnt_size*0.5)
     ax2.set_title(title+" Likelihood gain from # breakpoints")
     if ax is None:
         plt.savefig(title+'_Breakpts_Likelihood.pdf')
     # AIC
     if ax is None:
         fig, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
-        plt.rcParams['font.size'] = '18'
+        # 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.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
@@ -362,12 +368,14 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
     ax3.set_yscale('log')
     ax3.set_xlabel("# breakpoints", fontsize=fnt_size)
     ax3.set_ylabel("AIC")
-    ax3.legend(loc='best', fontsize = fnt_size*0.8)
+    ax3.legend(loc='best', fontsize = fnt_size*0.5)
     ax3.set_title(title+" AIC")
     if ax is None:
         plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')
+    print("S", S)
     return ax
-def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 10, ax = None):
+
+def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 10, ax = None, n_ticks = 10):
     """
     Use theta values as is to do basic plots.
     """
@@ -390,16 +398,14 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
         # intialize figure 1
         my_dpi = 300
         fnt_size = 18
+        # plt.rcParams['font.size'] = fnt_size
         fig, ax1 = 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)
     else:
         fnt_size = 12
+        # plt.rcParams['font.size'] = fnt_size
         ax1 = ax[0, 1]
         plt.subplots_adjust(wspace=0.3, hspace=0.3)
 
-    twin = ax1.twiny()
-
     plots = []
     for epoch, theta in epochs.items():
         groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist()
@@ -421,35 +427,32 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
                 prop = prop[::-1]
                 # print(prop, "\n", sum(prop))
         # normalise to N0 (N0 of epoch1)
+        x_ticks = ax1.get_xticks()
         for i in range(len(y)):
             y[i] = y[i]/N0
         # 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')
-        p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-.", 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
         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
-    if ax is None:
-        # arrange differently the second x axis if the plot is plain
-        twin.spines["bottom"].set_position(("axes", -0.15))
-    else:
-        # in a combined plot, more space between the fig and the axis
-        twin.spines["bottom"].set_position(("axes", -0.35))
+    #print(prop, "\n", sum(prop))
     #ax.legend(handles=[p0]+plots)
-    ax1.set_xlabel("# bin")
+    ax1.set_xlabel("# bin", fontsize=fnt_size)
     # Set the x-axis locator to reduce the number of ticks to 10
-    ax1.xaxis.set_major_locator(MaxNLocator(nbins=10))
-    twin.xaxis.set_major_locator(MaxNLocator(nbins=10))
-    ax1.set_ylabel("theta")
-    twin.set_ylabel("Proportion")
-    ax1.set_title("Title")
+    ax1.set_ylabel("theta", 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:
+        ax1.locator_params(nbins=n_ticks)
+    # new scale of ticks if too many values
+    cumul = 0
+    prop_cumul = []
+    for val in prop:
+        prop_cumul.append(val+cumul)
+        cumul = val+cumul
+    ax1.set_xticklabels([f'{x[k]}\n{val:.2f}' for k, val in enumerate(prop_cumul)])
     if ax is None:
         plt.savefig(title+'_raw'+str(k)+'.pdf')
     # fig 2 & 3
@@ -457,6 +460,7 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
         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]
@@ -487,43 +491,48 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
         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')
+        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')
+        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")
-    ax2.set_ylabel("theta")
-    ax2.set_title("Title")
+    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_xlabel("log Relative scale")
-    ax3.set_ylabel("theta")
-    ax3.set_title("Title")
+    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 ax
 
 def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True):
     my_dpi = 300
     # Add some extra space for the second axis at the bottom
+    #plt.rcParams['font.size'] = 18
     fig, axs = plt.subplots(3, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi)
+    #plt.rcParams['font.size'] = 12
     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
+    #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.close()
+    plt.clf()
     # 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)
+    plt.clf()
 
 if __name__ == "__main__":