def plot_all_stats(real_stats, real_dist, real_sfs, real_ld, sim_stats, sim_dist, sim_sfs, sim_ld, output):
fig, axes = plt.subplots(nrows=3, ncols=2, figsize=(7, 7))
color = COLORS[PREFIX]
ss_helpers.plot_sfs(axes.flatten()[0], real_sfs, sim_sfs, color, SIM_COLOR, pop=PREFIX, single=True)
ss_helpers.plot_dist(axes.flatten()[1], real_dist, sim_dist, color, SIM_COLOR, pop=PREFIX, single=True)
ss_helpers.plot_ld(axes.flatten()[2], real_ld, sim_ld, color, SIM_COLOR, pop=PREFIX, single=True)
for i in range(3):
ss_helpers.plot_generic(axes.flatten()[i+3], NAMES[i], real_stats[i], sim_stats[i], color, SIM_COLOR, pop=PREFIX, single=True)
plt.tight_layout()
if output != None:
plt.savefig(output, dpi=300)
else:
plt.show()
def plot_stats_threepop(real_stats1, real_dist1, real_sfs1, real_ld1,
real_stats2, real_dist2, real_sfs2, real_ld2,
real_stats3, real_dist3, real_sfs3, real_ld3,
sim_stats1, sim_dist1, sim_sfs1, sim_ld1, sim_stats2,
sim_dist2, sim_sfs2, sim_ld2, sim_stats3, sim_dist3,
sim_sfs3, sim_ld3, real_fst12, real_fst13, real_fst23,
sim_fst12, sim_fst13, sim_fst23, output):
fig, axes = plt.subplots(nrows=6, ncols=4, figsize=(14, 14))
pop_names = PREFIX.split("_")
POP1 = pop_names[0]
POP2 = pop_names[1]
POP3 = pop_names[2]
c1 = COLORS[POP1]
c2 = COLORS[POP2]
c3 = COLORS[POP3]
# pop 1
ss_helpers.plot_sfs(axes[0][0],
real_sfs1,
sim_sfs1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_dist(axes[0][1],
real_dist1,
sim_dist1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_ld(axes[1][0], real_ld1, sim_ld1, c1, SIM_COLOR, pop=POP1)
ss_helpers.plot_generic(axes[1][1],
NAMES[0],
real_stats1[0],
sim_stats1[0],
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_generic(axes[2][0],
NAMES[1],
real_stats1[1],
sim_stats1[1],
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_generic(axes[2][1],
NAMES[2],
real_stats1[2],
sim_stats1[2],
c1,
SIM_COLOR,
pop=POP1)
# pop 2
ss_helpers.plot_sfs(axes[0][2],
real_sfs2,
sim_sfs2,
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_dist(axes[0][3],
real_dist2,
sim_dist2,
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_ld(axes[1][2], real_ld2, sim_ld2, c2, SIM_COLOR, pop=POP2)
ss_helpers.plot_generic(axes[1][3],
NAMES[0],
real_stats2[0],
sim_stats2[0],
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_generic(axes[2][2],
NAMES[1],
real_stats2[1],
sim_stats2[1],
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_generic(axes[2][3],
NAMES[2],
real_stats2[2],
sim_stats2[2],
c2,
SIM_COLOR,
pop=POP2)
# pop 3
ss_helpers.plot_sfs(axes[3][2],
real_sfs3,
sim_sfs3,
c3,
SIM_COLOR,
pop=POP3)
ss_helpers.plot_dist(axes[3][3],
real_dist3,
sim_dist3,
c3,
SIM_COLOR,
pop=POP3)
ss_helpers.plot_ld(axes[4][2], real_ld3, sim_ld3, c3, SIM_COLOR, pop=POP3)
ss_helpers.plot_generic(axes[4][3],
NAMES[0],
real_stats3[0],
sim_stats3[0],
c3,
SIM_COLOR,
pop=POP3)
ss_helpers.plot_generic(axes[5][2],
NAMES[1],
real_stats3[1],
sim_stats3[1],
c3,
SIM_COLOR,
pop=POP3)
ss_helpers.plot_generic(axes[5][3],
NAMES[2],
real_stats3[2],
sim_stats3[2],
c3,
SIM_COLOR,
pop=POP3)
# fst 4
ss_helpers.plot_fst(axes[3][0], real_fst12, sim_fst12, POP1 + "/" + POP2,
"simulated", "purple", SIM_COLOR)
ss_helpers.plot_fst(axes[4][0], real_fst13, sim_fst13, POP1 + "/" + POP3,
"simulated", "purple", SIM_COLOR)
ss_helpers.plot_fst(axes[5][0], real_fst23, sim_fst23, POP2 + "/" + POP3,
"simulated", "purple", SIM_COLOR)
axes[3][1].axis('off')
axes[4][1].axis('off')
axes[5][1].axis('off')
# overall legend
pop1_real = mpatches.Patch(color=c1, label=POP1 + ' real data')
pop1_sim = mpatches.Patch(color=SIM_COLOR, label=POP1 + ' sim data')
pop2_real = mpatches.Patch(color=c2, label=POP2 + ' real data')
pop2_sim = mpatches.Patch(color=SIM_COLOR, label=POP2 + ' sim data')
pop3_real = mpatches.Patch(color=c3, label=POP3 + ' real data')
pop3_sim = mpatches.Patch(color=SIM_COLOR, label=POP3 + ' sim data')
axes[3][1].legend(handles=[pop1_real, pop1_sim], loc=10, prop={'size': 18})
axes[4][1].legend(handles=[pop2_real, pop2_sim], loc=10, prop={'size': 18})
axes[5][1].legend(handles=[pop3_real, pop3_sim], loc=10, prop={'size': 18})
plt.tight_layout()
if output != None:
plt.savefig(output, dpi=300)
else:
plt.show()
def plot_stats_twopop(real_stats1, real_dist1, real_sfs1, real_ld1, real_stats2, real_dist2, real_sfs2, real_ld2, real_fst, \
sim_stats1, sim_dist1, sim_sfs1, sim_ld1, sim_stats2, sim_dist2, sim_sfs2, sim_ld2, sim_fst, output, fsc=False):
pop_names = PREFIX.split("_")
POP1 = pop_names[0]
POP2 = pop_names[1]
c1 = COLORS[POP1]
c2 = COLORS[POP2]
pop1_real = mpatches.Patch(color=c1, label=POP1)
pop2_real = mpatches.Patch(color=c2, label=POP2)
pop2_sim = mpatches.Patch(color=SIM_COLOR, label='simulated data')
if not fsc:
fig, axes = plt.subplots(nrows=4, ncols=4, figsize=(14, 10))
axes_all = axes.flatten() # TODO don't flatten?
# row 1
ss_helpers.plot_sfs(axes_all[0],
real_sfs1,
sim_sfs1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_dist(axes_all[1],
real_dist1,
sim_dist1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_sfs(axes_all[2],
real_sfs2,
sim_sfs2,
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_dist(axes_all[3],
real_dist2,
sim_dist2,
c2,
SIM_COLOR,
pop=POP2)
# row 2
ss_helpers.plot_ld(axes_all[4],
real_ld1,
sim_ld1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_generic(axes_all[5],
NAMES[0],
real_stats1[0],
sim_stats1[0],
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_ld(axes_all[6],
real_ld2,
sim_ld2,
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_generic(axes_all[7],
NAMES[0],
real_stats2[0],
sim_stats2[0],
c2,
SIM_COLOR,
pop=POP2)
# row 3
ss_helpers.plot_generic(axes_all[8],
NAMES[1],
real_stats1[1],
sim_stats1[1],
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_generic(axes_all[9],
NAMES[2],
real_stats1[2],
sim_stats1[2],
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_generic(axes_all[10],
NAMES[1],
real_stats2[1],
sim_stats2[1],
c2,
SIM_COLOR,
pop=POP2)
ss_helpers.plot_generic(axes_all[11],
NAMES[2],
real_stats2[2],
sim_stats2[2],
c2,
SIM_COLOR,
pop=POP2)
# row 4
ss_helpers.plot_fst(axes_all[13], real_fst, sim_fst, POP1 + "/" + POP2,
"simulated", "purple", SIM_COLOR)
axes_all[12].axis('off')
axes_all[14].axis('off')
axes_all[15].axis('off')
# overall legend
pop1_real = mpatches.Patch(color=c1, label=POP1 + ' real data')
pop1_sim = mpatches.Patch(color=SIM_COLOR, label=POP1 + ' sim data')
pop2_real = mpatches.Patch(color=c2, label=POP2 + ' real data')
pop2_sim = mpatches.Patch(color=SIM_COLOR, label=POP2 + ' sim data')
axes_all[12].legend(handles=[pop1_real, pop1_sim],
loc=10,
prop={'size': 18})
axes_all[15].legend(handles=[pop2_real, pop2_sim],
loc=10,
prop={'size': 18})
# fastsimcoal
else:
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(10.5, 2.5))
axes_all = axes.flatten() # TODO don't flatten?
# row 1
ss_helpers.plot_sfs(axes_all[0],
real_sfs1,
sim_sfs1,
c1,
SIM_COLOR,
pop=POP1)
ss_helpers.plot_sfs(axes_all[1],
real_sfs2,
sim_sfs2,
c2,
SIM_COLOR,
pop=POP2)
axes_all[2].axis('off')
axes_all[2].legend(handles=[pop1_real, pop2_real, pop2_sim],
loc=10,
prop={'size': 16})
plt.tight_layout()
if output != None:
plt.savefig(output, dpi=300)
else:
plt.show()