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Fixing some scaling for swp2 output

master
tforest 2024-02-29 00:59:25 +01:00
parent 25d7ef0858
commit 1848102140
1 changed files with 98 additions and 36 deletions
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swp2.py
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@ -176,7 +176,7 @@ def plot_all_epochs_thetafolder(full_dict, mu, tgen, title = "Title",
ax1.set_title(title) ax1.set_title(title)
breaks = len(full_dict['all_epochs']['plots']) breaks = len(full_dict['all_epochs']['plots'])
if ax is None: if ax is None:
plt.savefig(title+'_'+str(breaks+1)+'_epochs.pdf') plt.savefig(title+'_best_'+str(breaks+1)+'_epochs.pdf')
# plot likelihood against nb of breakpoints # plot likelihood against nb of breakpoints
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)
@ -299,7 +299,15 @@ def save_all_epochs_thetafolder(folder_path, mu, tgen, title = "Title", theta_sc
# number of monomorphic sites # 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)
my_n = len(SFS_stored)*2
print("n=",my_n)
an = 1
for i in range(2, my_n):
an +=1.0/i
print("an=", an, "theta_w", S/an, "theta_w_p_site", (S/an)/L)
# compute Ln # compute Ln
Ln = log_facto(S+S0) - log_facto(S0) + np.log(float(S0)/(S+S0)) * S0 Ln = log_facto(S+S0) - log_facto(S0) + np.log(float(S0)/(S+S0)) * S0
for xi in range(0, len(SFS_stored)): for xi in range(0, len(SFS_stored)):
@ -413,6 +421,25 @@ def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
cumul = val+cumul cumul = val+cumul
prop = prop_cumul prop = prop_cumul
# print("raw stairs", plots[3])
# ###########
# time = []
# for k in plots[0][0]:
# k = int(k)
# dt = 2.0/(k*(k-1))
# time.append(2.0/(k*(k-1)))
# Ne = []
# for values in plots:
# Ne.append(np.array(values[1])/(4*mu))
# print(time)
# print(Ne[3])
lines_fig2 = [] lines_fig2 = []
for epoch, theta in best_epochs.items(): for epoch, theta in best_epochs.items():
groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist() groups = np.array(list(theta.values()), dtype=object)[:, 1].tolist()
@ -423,24 +450,33 @@ def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
x += group[::-1] x += group[::-1]
y += list(np.repeat(thetas[i], len(group))) y += list(np.repeat(thetas[i], len(group)))
if epoch == 0: if epoch == 0:
N0 = y[0] # watterson theta
theta_w = y[0]
if theta_scale : if theta_scale :
for i in range(len(y)): for i in range(len(y)):
y[i] = y[i]/N0 y[i] = y[i]/N0
for i in range(len(y)):
y[i] = y[i]/(4*mu)
x_2 = [] x_2 = []
T = 0 T = 0
for i in range(len(x)): for i in range(len(x)):
x[i] = int(x[i]) x[i] = int(x[i])
# compute the times as: theta_k / (k*(k-1)) # compute the times as: theta_k / (k*(k-1))
for i in range(0, len(x)): for i in range(0, len(x)):
T += y[i] / (x[i]*(x[i]-1)) T += y[i]*2 / (x[i]*(x[i]-1))
x_2.append(T) x_2.append(T)
# Save plotting (fig 2) # Save plotting (fig 2)
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 = x_2, y p2 = x_2, y
lines_fig2.append(p2) lines_fig2.append(p2)
# print("breaks=", epoch, "scaled_theta", lines_fig2[10])
# print(lines_fig2[3][1][0]/(4*mu))
# print(np.array(lines_fig2[3][1])/lines_fig2[3][1][0])
# print("size list y=", len(lines_fig2[3][1]))
#exit(0)
if input == None: if input == None:
saved_plots = {"raw_stairs":plots, "scaled_stairs":lines_fig2, saved_plots = {"raw_stairs":plots, "scaled_stairs":lines_fig2,
"prop":prop} "prop":prop}
@ -458,9 +494,9 @@ def save_k_theta(folder_path, mu, tgen, title = "Title", theta_scale = True,
return saved_plots return saved_plots
def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax = None, n_ticks = 10, subset = None, theta_scale = False): def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax = None, n_ticks = 10, subset = None, theta_scale = False):
recent_limit_years = 500 recent_limit_years = 100
# recent limit in coal. time # recent limit in coal. time
recent_limit = recent_limit_years/tgen*mu recent_limit = recent_limit_years/tgen
# nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1) # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1)
nb_epochs = len(plot_lines) nb_epochs = len(plot_lines)
# fig 2 & 3 # fig 2 & 3
@ -480,9 +516,9 @@ def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax =
#plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi) #plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
if swp2_lines: if swp2_lines:
for k in range(len(swp2_lines[0])): for k in range(len(swp2_lines[0])):
swp2_lines[0][k] = swp2_lines[0][k]/tgen*mu swp2_lines[0][k] = swp2_lines[0][k]/tgen
for k in range(len(swp2_lines[1])): for k in range(len(swp2_lines[1])):
swp2_lines[1][k] = swp2_lines[1][k]*4*mu swp2_lines[1][k] = swp2_lines[1][k]
# x2_plot, y2_plot = plot_straight_x_y(swp2_lines[0],swp2_lines[1]) # x2_plot, y2_plot = plot_straight_x_y(swp2_lines[0],swp2_lines[1])
x2_plot, y2_plot = swp2_lines[0], swp2_lines[1] x2_plot, y2_plot = swp2_lines[0], swp2_lines[1]
p2, = ax2.plot(x2_plot, y2_plot, linestyle="-", alpha=0.75, lw=2, label = 'swp2', color="black") p2, = ax2.plot(x2_plot, y2_plot, linestyle="-", alpha=0.75, lw=2, label = 'swp2', color="black")
@ -508,14 +544,14 @@ def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax =
# skip the base 0 points x_plot[0:3] # skip the base 0 points x_plot[0:3]
t_max_below_limit = 0 t_max_below_limit = 0
t_min_below_limit = 1 t_min_below_limit = recent_limit
recent_change = False recent_change = False
for t in x[1:]: for t in x[1:]:
if t <= recent_limit: if t <= recent_limit:
recent_change = True recent_change = True
t_max_below_limit = max(t_max_below_limit, t) t_max_below_limit = max(t_max_below_limit, t)
t_min_below_limit = min(t_min_below_limit, t) t_min_below_limit = min(t_min_below_limit, t)
Ne_max_below_limit = y[x.index(t_max_below_limit)] Ne_max_below_limit = y[min(x.index(t_max_below_limit)+1, len(y)-1)]
Ne_min_below_limit = y[x.index(t_min_below_limit)] Ne_min_below_limit = y[x.index(t_min_below_limit)]
if recent_change: if recent_change:
print(f"\n{breaks} breaks ; This is below the recent limit of {recent_limit_years} years:\n", print(f"\n{breaks} breaks ; This is below the recent limit of {recent_limit_years} years:\n",
@ -547,6 +583,8 @@ def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax =
lines_fig3.append(p3) lines_fig3.append(p3)
# put the vertical line of the "recent" time limit # put the vertical line of the "recent" time limit
ax3.axvline(x=recent_limit, linestyle="--") ax3.axvline(x=recent_limit, linestyle="--")
ax3.axvline(x=recent_limit/2, linestyle="--", color="green")
if theta_scale: if theta_scale:
xlabel = "Theta scaled by N0" xlabel = "Theta scaled by N0"
ylabel = "Theta scaled by N0" ylabel = "Theta scaled by N0"
@ -557,26 +595,36 @@ def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax =
# if not ax, then use the plt syntax, not ax... # if not ax, then use the plt syntax, not ax...
plt.xlabel(xlabel, fontsize=fnt_size) plt.xlabel(xlabel, fontsize=fnt_size)
plt.ylabel(ylabel, fontsize=fnt_size) plt.ylabel(ylabel, fontsize=fnt_size)
#plt.xlim(left=0) plt.gca().set_xlim(0, recent_limit * 3)
if recent_change:
plt.ylim(Ne_min_below_limit/3, Ne_max_below_limit *3)
else:
plt.ylim(y2_plot[0]/3, y2_plot[0])
# plt.ylim(0, max(max_y+(max_y*0.05), max(swp2_lines[1])+(max(swp2_lines[1])*0.05)))
#plt.xlim(0, recent_limit * 3)
#xlim_val = plt.gca().get_xlim() #xlim_val = plt.gca().get_xlim()
#x_ticks = list(plt.xticks())[0] x_ticks = list(plt.xticks())[0]
plt.xlim(min(min_x,min(swp2_lines[0])), max(max(swp2_lines[0]), max_x)) # plt.xlim(min(min_x,min(swp2_lines[0])), max(max(swp2_lines[0]), max_x))
x_ticks = list(plt.gca().get_xticks()) # x_ticks = list(plt.gca().get_xticks())
plt.gca().set_xticks(x_ticks) # plt.gca().set_xticks(x_ticks)
# plt.xticks(x_ticks) # plt.xticks(x_ticks)
# plt.gca().set_xlim(xlim_val) # plt.gca().set_xlim(xlim_val)
plt.gca().set_xticklabels([f'{k:.0e}\n{k/(mu):.0e}\n{k/(mu)*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5) # plt.gca().set_xticklabels([f'{k:.0e}\n{k/(mu):.0e}\n{k/(mu)*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5)
plt.gca().set_xticklabels([f'{k:.1f}\n{k*tgen:.1f}' for k in x_ticks], fontsize = fnt_size*0.5)
# rescale y to effective pop size # rescale y to effective pop size
# ylim_val = plt.gca().get_ylim() # ylim_val = plt.gca().get_ylim()
plt.ylim(min(min_y,min(swp2_lines[1])), max(max_y+(max_y*0.05), max(swp2_lines[1])+(max(swp2_lines[1])*0.05))) # plt.ylim(min(min_y,min(swp2_lines[1])), max(max_y+(max_y*0.05), max(swp2_lines[1])+(max(swp2_lines[1])*0.05)))
y_ticks = list(plt.yticks())[0] # y_ticks = list(plt.yticks())[0]
plt.gca().set_yticks(y_ticks) # plt.gca().set_yticks(y_ticks)
# plt.gca().set_ylim(ylim_val) # plt.gca().set_ylim(ylim_val)
plt.yticks(y_ticks) # plt.yticks(y_ticks)
plt.gca().set_yticklabels([f'{k/(4*mu):.0e}' for k in y_ticks], fontsize = fnt_size*0.5) # plt.gca().set_yticklabels([f'{k/(4*mu):.0e}' for k in y_ticks], fontsize = fnt_size*0.5)
plt.title(title, fontsize=fnt_size) # plt.title(title, fontsize=fnt_size)
plt.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5) # plt.legend(handles=lines_fig2, loc='best', fontsize = fnt_size*0.5)
plt.text(-0.13, -0.135, 'Coal. time\nGen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes) # # plt.text(-0.13, -0.135, 'Coal. time\nGen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes)
plt.text(-0.13, -0.135, 'Gen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes)
plt.subplots_adjust(bottom=0.2) # Adjust the value as needed plt.subplots_adjust(bottom=0.2) # Adjust the value as needed
plt.savefig(title+'_plotB_'+str(nb_epochs)+'_epochs.pdf') plt.savefig(title+'_plotB_'+str(nb_epochs)+'_epochs.pdf')
# close fig2 to save memory # close fig2 to save memory
@ -594,16 +642,30 @@ def plot_scaled_theta(plot_lines, prop, title, mu, tgen, swp2_lines = None, ax =
ax3.set_xscale('log') ax3.set_xscale('log')
ax3.set_yscale('log') ax3.set_yscale('log')
# Scale the x-axis # Scale the x-axis
x_ticks = list(ax3.get_xticks()) # x_ticks = list(ax3.get_xticks())
ax3.set_xticks(x_ticks) # ax3.set_xticks(x_ticks)
ax3.set_xlim(min(min(x_ticks), min(swp2_lines[0])), max(max_x, max(swp2_lines[0]))) # x_ticks = [i for i in range(0.1,max(max_x, max(swp2_lines[0]))), ]
ax3.set_xticklabels([f'{k:.0e}\n{k/(mu):.0e}\n{k/(mu)*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5) # ax3.set_xticks(x_ticks)
ax3.set_xlim(0.1, max(max_x, max(swp2_lines[0])))
x_ticks = ax3.get_xticks()
# ax3.set_xlim(min(min(x_ticks), min(swp2_lines[0])), max(max_x, max(swp2_lines[0])))
# ax3.set_xlim(1, max(max_x, max(swp2_lines[0])))
# ax3.set_xticklabels([f'{k:.0e}\n{k/(mu):.0e}\n{k/(mu)*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5)
# ax3.set_xticklabels([f'{k/(mu):.0e}\n{k/(mu)*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5)
ax3.set_xticklabels([f'{k:.0e}\n{k*tgen:.0e}' for k in x_ticks], fontsize = fnt_size*0.5)
# rescale y to effective pop size # rescale y to effective pop size
y_ticks = list(ax3.get_yticks()) # y_ticks = list(ax3.get_yticks())
ax3.set_yticks(y_ticks) # ax3.set_yticks(y_ticks)
ax3.set_ylim(min(min(y_ticks), min(swp2_lines[1])), max(max_y+(max_y*0.5), max(swp2_lines[1])+(max(swp2_lines[1])*0.5))) # ax3.set_ylim(min(min(y_ticks), min(swp2_lines[1])), max(max_y+(max_y*0.5), max(swp2_lines[1])+(max(swp2_lines[1])*0.5)))
ax3.set_yticklabels([f'{k/(4*mu):.0e}' for k in y_ticks], fontsize = fnt_size*0.5) # ax3.set_ylim(1, max(max_y, max(swp2_lines[1])))
plt.text(-0.13, -0.135, 'Coal. time\nGen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes) ax3.set_ylim(1, max(max_y+(max_y*0.5), max(swp2_lines[1])+(max(swp2_lines[1])*0.5)))
# ax3.set_yticklabels([f'{k/(4*mu):.0e}' for k in y_ticks], fontsize = fnt_size*0.5)
# plt.text(-0.13, -0.135, 'Coal. time\nGen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes)
# plt.text(-0.13, -0.135, 'Gen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes)
plt.text(-0.13, -0.085, 'Gen. time\nYears', ha='left', va='bottom', transform=ax3.transAxes)
plt.subplots_adjust(bottom=0.2) # Adjust the value as needed plt.subplots_adjust(bottom=0.2) # Adjust the value as needed
if ax is None: if ax is None:
# nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1) # nb of plot_lines represent the number of epochs stored (len(plot_lines) = #breaks+1)
@ -638,7 +700,7 @@ def plot_raw_stairs(plot_lines, prop, title, ax = None, n_ticks = 10, rescale =
x,y = plot x,y = plot
x_plot, y_plot = plot_straight_x_y(x,y) x_plot, y_plot = plot_straight_x_y(x,y)
p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(breaks)+' brks') p, = ax1.plot(x_plot, y_plot, 'o', linestyle="-", alpha=0.75, lw=2, label = str(breaks)+' brks')
print("breaks=", breaks, "theta0", y[0])
# 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)
x_ticks = x x_ticks = x