Coalescent Simulator Interact

## Description

This is a sage interact for a coalescent simulator.

## Sage Cell

#### Code

``````def next_gen(x, selection=1.0):
'''Creates the next generation from the previous; also returns parent-child indexing list'''
next_x = []
for ind in range(len(x)):
if random() < (1 + selection)/len(x):
rind = 0
else:
rind = int(round(random()*(len(x)-1)+1/2))
next_x.append((x[rind],rind))
next_x.sort()
return [[x for x in next_x],[x for x in next_x]]
def coal_plot(some_data):
'''Creates a graphics object from coalescent data'''
gens = some_data
inds = some_data
gen_lines = line([[0,0]])
pts = Graphics()
ngens = len(gens)
gen_size = len(gens)
for x in range(gen_size):
pts += point((x,ngens-1), hue = gens[x]/float(gen_size*1.1))
p_frame = line([[-.5,-.5],[-.5,ngens-.5], [gen_size-.5,ngens-.5], [gen_size-.5,-.5], [-.5,-.5]])
for g in range(1,ngens):
for x in range(gen_size):
old_x = inds[g-1][x]
gen_lines += line([[x,ngens-g-1],[old_x,ngens-g]], hue = gens[g-1][old_x]/float(gen_size*1.1))
pts += point((x,ngens-g-1), hue = gens[g][x]/float(gen_size*1.1))
return pts+gen_lines+p_frame
d_field = RealField(10)
@interact
def coalescents(pop_size = slider(2,100,1,15,'Population size'), selection = slider(-1,1,.1,0, 'Selection for first taxon'), s = selector(['Again!'], label='Refresh', buttons=True)):
print('Population size: ' + str(pop_size))
print('Selection coefficient for first taxon: ' + str(d_field(selection)))
start = [i for i in range(pop_size)]
gens = [start]
inds = []
while gens[-1] != gens[-1][-1]:
g_index = len(gens) - 1
n_gen = next_gen(gens[g_index], selection = selection)
gens.append(n_gen)
inds.append(n_gen)
coal_data1 = [gens,inds]
print('Generations until coalescence: ' + str(len(gens)))
show(coal_plot(coal_data1), axes = False, figsize = [8, 4.0*len(gens)/pop_size], ymax = len(gens)-1)```
```

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