Fixing plot font size issues
tforest
parent
2e4aca9951
commit
6287f2aa71
105
swp2.py
105
swp2.py
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@ -7,7 +7,7 @@ from matplotlib.backends.backend_pdf import PdfPages
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from matplotlib.ticker import MaxNLocator
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import io
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from mpl_toolkits.axes_grid1.inset_locator import inset_axes
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from matplotlib.ticker import MultipleLocator
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def log_facto(k):
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k = int(k)
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if k > 1e6:
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@ -259,10 +259,11 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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# intialize figure
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my_dpi = 300
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fnt_size = 18
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# plt.rcParams['font.size'] = fnt_size
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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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# 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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ax1.set_yscale('log')
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@ -293,26 +294,30 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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best10_plots = sorted(plots_likelihoods)[:10]
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top_plot_lik = str(best10_plots[0])
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plot_handles = []
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# plt.rcParams['font.size'] = fnt_size
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p0, = ax1.plot(top_plots[top_plot_lik][0], top_plots[top_plot_lik][1], 'o', linestyle = "-",
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alpha=1, lw=2, label = str(top_plots[top_plot_lik][2])+' epoch | Lik='+top_plot_lik)
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alpha=1, lw=2, label = str(top_plots[top_plot_lik][2])+' brks | Lik='+top_plot_lik)
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plot_handles.append(p0)
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for k, plot_Lk in enumerate(best10_plots[1:]):
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plot_Lk = str(plot_Lk)
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# plt.rcParams['font.size'] = fnt_size
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p, = ax1.plot(top_plots[plot_Lk][0], top_plots[plot_Lk][1], 'o', linestyle = "--",
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alpha=1/(k+1), lw=1.5, label = str(top_plots[plot_Lk][2])+' epoch | Lik='+plot_Lk)
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alpha=1/(k+1), lw=1.5, label = str(top_plots[plot_Lk][2])+' brks | Lik='+plot_Lk)
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plot_handles.append(p)
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if theta_scale:
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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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ax1.set_xlabel("Coal. time", fontsize=fnt_size)
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ax1.set_ylabel("Pop. size scaled by N0", fontsize=fnt_size)
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# recent_scale_lower_bound = 0.01
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# recent_scale_upper_bound = 0.1
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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.set_xlabel("Time (years)")
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plt.set_ylabel("Individuals (N)")
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plt.set_xlabel("Time (years)", fontsize=fnt_size)
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plt.set_ylabel("Individuals (N)", fontsize=fnt_size)
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ax1.set_xlim(1e-5, 1)
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# plt.rcParams['font.size'] = fnt_size
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# print(fnt_size, "rcParam font.size=", plt.rcParams['font.size'])
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ax1.legend(handles = plot_handles, 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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@ -335,24 +340,25 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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# basic plot likelihood
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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.rcParams['font.size'] = fnt_size
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else:
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plt.rcParams['font.size'] = fnt_size
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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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ax2.axhline(y=-Ln, linestyle = "-.", color = "red", label = "$-\log\mathcal{L}$ = "+str(round(-Ln, 2)))
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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*0.8)
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ax2.set_ylabel("$-\log\mathcal{L}$", fontsize=fnt_size)
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ax2.legend(loc='best', fontsize = fnt_size*0.5)
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ax2.set_title(title+" Likelihood gain from # breakpoints")
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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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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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# plt.rcParams['font.size'] = '18'
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else:
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#plt.rcParams['font.size'] = fnt_size
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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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ax3.plot(np.array(brkpt_lik)[:, 0], AIC, 'o', linestyle = "dotted", lw=2)
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@ -362,12 +368,14 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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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*0.8)
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ax3.legend(loc='best', fontsize = fnt_size*0.5)
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ax3.set_title(title+" AIC")
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if ax is None:
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plt.savefig(title+'_Breakpts_Likelihood_AIC.pdf')
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print("S", S)
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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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def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True, breaks_max = 10, ax = None, n_ticks = 10):
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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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@ -390,16 +398,14 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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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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# plt.rcParams['font.size'] = fnt_size
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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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# plt.rcParams['font.size'] = fnt_size
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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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twin = ax1.twiny()
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plots = []
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for epoch, theta in epochs.items():
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groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist()
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@ -421,35 +427,32 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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prop = prop[::-1]
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# print(prop, "\n", sum(prop))
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# normalise to N0 (N0 of epoch1)
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x_ticks = ax1.get_xticks()
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for i in range(len(y)):
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y[i] = y[i]/N0
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# plot
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x_plot, y_plot = plot_straight_x_y(x, y)
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#plt.plot(x, y, 'o', linestyle="dotted", alpha=0.75, lw=2, label = str(epoch)+' brks')
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p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
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p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks')
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# add plot to the list of all plots to superimpose
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plots.append(p)
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# virtual line to get the second x axis for proportions
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p0, = twin.plot(prop, y, alpha = 0, label="Proportion")
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# Move twinned axis ticks and label from top to bottom
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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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#print(prop, "\n", sum(prop))
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#ax.legend(handles=[p0]+plots)
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ax1.set_xlabel("# bin")
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ax1.set_xlabel("# bin", fontsize=fnt_size)
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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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twin.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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ax1.set_title("Title")
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ax1.set_ylabel("theta", fontsize=fnt_size)
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ax1.set_title("Title", fontsize=fnt_size)
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ax1.legend(handles=plots, loc='best', fontsize = fnt_size*0.5)
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ax1.set_xticks(x_ticks)
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if len(prop) >= 18:
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ax1.locator_params(nbins=n_ticks)
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# new scale of ticks if too many values
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cumul = 0
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prop_cumul = []
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for val in prop:
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prop_cumul.append(val+cumul)
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cumul = val+cumul
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ax1.set_xticklabels([f'{x[k]}\n{val:.2f}' for k, val in enumerate(prop_cumul)])
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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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@ -457,6 +460,7 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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fig2, ax2 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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fig3, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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else:
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# plt.rcParams['font.size'] = fnt_size
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# place of plots on the grid
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ax2 = ax[1,0]
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ax3 = ax[1,1]
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@ -487,43 +491,48 @@ def plot_test_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
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x_2 = [0]+x_2
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y = [y[0]]+y
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x2_plot, y2_plot = plot_straight_x_y(x_2, y)
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p2, = ax2.plot(x2_plot, y2_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
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p2, = ax2.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks')
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lines_fig2.append(p2)
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# Plotting (fig 3) which is the same but log scale for x
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p3, = ax3.plot(x2_plot, y2_plot, 'o', linestyle="-.", alpha=0.75, lw=2, label = str(epoch)+' brks')
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p3, = ax3.plot(x2_plot, y2_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(epoch)+' brks')
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lines_fig3.append(p3)
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ax2.set_xlabel("Relative scale")
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ax2.set_ylabel("theta")
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ax2.set_title("Title")
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ax2.set_xlabel("Relative scale", fontsize=fnt_size)
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ax2.set_ylabel("theta", fontsize=fnt_size)
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ax2.set_title("Title", fontsize=fnt_size)
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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 Relative scale")
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ax3.set_ylabel("theta")
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ax3.set_title("Title")
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ax3.set_yscale('log')
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ax3.set_xlabel("log Relative scale", fontsize=fnt_size)
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ax3.set_ylabel("theta", fontsize=fnt_size)
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ax3.set_title("Title", fontsize=fnt_size)
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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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plt.clf()
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# return plots
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return ax
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def combined_plot(folder_path, mu, tgen, breaks, title = "Title", theta_scale = True):
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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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#plt.rcParams['font.size'] = 18
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fig, axs = plt.subplots(3, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi)
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#plt.rcParams['font.size'] = 12
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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=0.7) # 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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plt.close()
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plt.clf()
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# second call for individual plots
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plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = None)
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plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = None)
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plt.clf()
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if __name__ == "__main__":
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