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Fixing plot font size issues

master
tforest 2023-12-05 17:04:36 +01:00
parent 2e4aca9951
commit 6287f2aa71
1 changed files with 57 additions and 48 deletions
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105
swp2.py
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@ -7,7 +7,7 @@ from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.ticker import MaxNLocator from matplotlib.ticker import MaxNLocator
import io import io
from mpl_toolkits.axes_grid1.inset_locator import inset_axes from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from matplotlib.ticker import MultipleLocator
def log_facto(k): def log_facto(k):
k = int(k) k = int(k)
if k > 1e6: if k > 1e6:
@ -259,10 +259,11 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
# intialize figure # intialize figure
my_dpi = 300 my_dpi = 300
fnt_size = 18 fnt_size = 18
# plt.rcParams['font.size'] = fnt_size
fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
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[0,0]
#ax1.set_xlim(1e-3, 1) #ax1.set_xlim(1e-3, 1)
ax1.set_yscale('log') 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] best10_plots = sorted(plots_likelihoods)[:10]
top_plot_lik = str(best10_plots[0]) top_plot_lik = str(best10_plots[0])
plot_handles = [] 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 = "-", 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) plot_handles.append(p0)
for k, plot_Lk in enumerate(best10_plots[1:]): for k, plot_Lk in enumerate(best10_plots[1:]):
plot_Lk = str(plot_Lk) 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 = "--", 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) plot_handles.append(p)
if theta_scale: if theta_scale:
ax1.set_xlabel("Coal. time") ax1.set_xlabel("Coal. time", fontsize=fnt_size)
ax1.set_ylabel("Pop. size scaled by N0") ax1.set_ylabel("Pop. size scaled by N0", fontsize=fnt_size)
# recent_scale_lower_bound = 0.01 # recent_scale_lower_bound = 0.01
# recent_scale_upper_bound = 0.1 # recent_scale_upper_bound = 0.1
# ax1.axvline(x=recent_scale_lower_bound) # ax1.axvline(x=recent_scale_lower_bound)
# ax1.axvline(x=recent_scale_upper_bound) # ax1.axvline(x=recent_scale_upper_bound)
else: else:
# years # years
plt.set_xlabel("Time (years)") plt.set_xlabel("Time (years)", fontsize=fnt_size)
plt.set_ylabel("Individuals (N)") plt.set_ylabel("Individuals (N)", fontsize=fnt_size)
ax1.set_xlim(1e-5, 1) 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.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:
@ -335,24 +340,25 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
# 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)
plt.rcParams['font.size'] = '18' # 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[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)
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')
ax2.set_xlabel("# breakpoints", fontsize=fnt_size) ax2.set_xlabel("# breakpoints", fontsize=fnt_size)
ax2.set_ylabel("$-\log\mathcal{L}$") ax2.set_ylabel("$-\log\mathcal{L}$", fontsize=fnt_size)
ax2.legend(loc='best', fontsize = fnt_size*0.8) ax2.legend(loc='best', fontsize = fnt_size*0.5)
ax2.set_title(title+" Likelihood gain from # breakpoints") 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
if ax is None: if ax is None:
fig, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) 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: else:
#plt.rcParams['font.size'] = fnt_size
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)
@ -362,12 +368,14 @@ def plot_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
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*0.8) ax3.legend(loc='best', fontsize = fnt_size*0.5)
ax3.set_title(title+" AIC") 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')
print("S", S)
return ax 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. 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 # intialize figure 1
my_dpi = 300 my_dpi = 300
fnt_size = 18 fnt_size = 18
# plt.rcParams['font.size'] = fnt_size
fig, ax1 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) 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: else:
fnt_size = 12 fnt_size = 12
# plt.rcParams['font.size'] = fnt_size
ax1 = ax[0, 1] ax1 = ax[0, 1]
plt.subplots_adjust(wspace=0.3, hspace=0.3) plt.subplots_adjust(wspace=0.3, hspace=0.3)
twin = ax1.twiny()
plots = [] plots = []
for epoch, theta in epochs.items(): for epoch, theta in epochs.items():
groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist() 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] prop = prop[::-1]
# print(prop, "\n", sum(prop)) # print(prop, "\n", sum(prop))
# normalise to N0 (N0 of epoch1) # normalise to N0 (N0 of epoch1)
x_ticks = ax1.get_xticks()
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) 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_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 # 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 #print(prop, "\n", sum(prop))
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))
#ax.legend(handles=[p0]+plots) #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 # Set the x-axis locator to reduce the number of ticks to 10
ax1.xaxis.set_major_locator(MaxNLocator(nbins=10)) ax1.set_ylabel("theta", fontsize=fnt_size)
twin.xaxis.set_major_locator(MaxNLocator(nbins=10)) ax1.set_title("Title", fontsize=fnt_size)
ax1.set_ylabel("theta")
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)
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: if ax is None:
plt.savefig(title+'_raw'+str(k)+'.pdf') plt.savefig(title+'_raw'+str(k)+'.pdf')
# fig 2 & 3 # 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) 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) fig3, ax3 = plt.subplots(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
else: else:
# plt.rcParams['font.size'] = fnt_size
# place of plots on the grid # place of plots on the grid
ax2 = ax[1,0] ax2 = ax[1,0]
ax3 = ax[1,1] 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 x_2 = [0]+x_2
y = [y[0]]+y y = [y[0]]+y
x2_plot, y2_plot = plot_straight_x_y(x_2, 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) 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(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) lines_fig3.append(p3)
ax2.set_xlabel("Relative scale") ax2.set_xlabel("Relative scale", fontsize=fnt_size)
ax2.set_ylabel("theta") ax2.set_ylabel("theta", fontsize=fnt_size)
ax2.set_title("Title") 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')
ax3.set_xscale('log') ax3.set_xscale('log')
ax3.set_xlabel("log Relative scale") ax3.set_yscale('log')
ax3.set_ylabel("theta") ax3.set_xlabel("log Relative scale", fontsize=fnt_size)
ax3.set_title("Title") 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) 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')
plt.clf()
# return plots # return plots
return ax return ax
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
#plt.rcParams['font.size'] = 18
fig, axs = plt.subplots(3, 2, figsize=(5000/my_dpi, 2970/my_dpi), dpi=my_dpi) 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_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() plt.clf()
# second call for individual plots # second call for individual plots
plot_all_epochs_thetafolder(folder_path, mu, tgen, title, theta_scale, ax = None) 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) plot_test_theta(folder_path, mu, tgen, title, theta_scale, breaks_max = breaks, ax = None)
plt.clf()
if __name__ == "__main__": if __name__ == "__main__":