Issue 20 visualize (#25)

* approaching #20

* solving #20

* fighting #20

* solved #20

* solved #20

hamazaki1990/individual.py

@@ -1,3 +1,6 @@
+from decimal import Decimal
+
+
 class Individual:
     def __init__(self, n, f=1.0):
         self._id = n
@@ -11,17 +14,14 @@ def get_fitness(self):
 
     def __repr__(self):
         return str(self._id)
+        return Decimal(self._fitness)
 
 
 def main():
     ind = Individual(42)
     print(ind.get_id())
     print(ind.get_fitness())
 
-    ind2 = Individual(30, 0.8)
-    print(ind2.get_id())
-    print(ind2.get_fitness())
-
 
 if __name__ == '__main__':
     main()

hamazaki1990/population.py

@@ -16,12 +16,17 @@ def __init__(self, n, mutantrate=0, s=0):
         wild_inds = [Individual(x) for x in range(num_mutant, n)]
         self._inds = mutant_inds + wild_inds
 
-    def print_ids(self):
-        print(self._inds)
+    def get_ids(self):
+        return self._inds
 
-    def print_fitness(self):
+    def get_fitnesses(self):
         fitness = [x.get_fitness() for x in self._inds]
-        print(fitness)
+        return fitness
+
+    def get_mutantfreq(self):
+        fitness = [x.get_fitness() for x in self._inds]
+        mutantfreq = 1 - fitness.count(1.0)/len(fitness)
+        return mutantfreq
 
     def next_genwf(self):
         fitness = [x.get_fitness() for x in self._inds]
@@ -46,45 +51,60 @@ def is_not_fixed(self):
         else:
             return False
 
+    def mutation_is_not_fixed(self):
+        fitness = [x.get_fitness() for x in self._inds]
+        for x in range(1, len(fitness)):
+            if fitness[0] != fitness[x]:
+                return True
+        else:
+            return False
+
 
 def main():
     p1_1 = Population(10)
-    p1_1.print_ids()
-    p1_1.print_fitness()
+    print(p1_1.get_ids())
+    print(p1_1.get_fitnesses())
     print(p1_1.is_not_fixed())
+    print(p1_1.mutation_is_not_fixed())
 
     for x in range(20):
         p1_1.next_genwf()
-        p1_1.print_ids()
-        p1_1.print_fitness()
+        print(p1_1.get_ids())
+        print(p1_1.get_fitnesses())
     print(p1_1.is_not_fixed())
+    print(p1_1.mutation_is_not_fixed())
 
     p1_2 = Population(10, 0.3, 0.2)
-    p1_2.print_ids()
-    p1_2.print_fitness()
+    print(p1_2.get_ids())
+    print(p1_2.get_fitnesses())
+    print(p1_2.is_not_fixed())
+    print(p1_2.mutation_is_not_fixed())
+    print(p1_2.get_mutantfreq())
 
     for x in range(20):
         p1_2.next_genwf()
-        p1_2.print_ids()
-    p1_2.print_fitness()
+        print(p1_2.get_ids())
+    print(p1_2.get_fitnesses())
+    print(p1_2.is_not_fixed())
+    print(p1_2.mutation_is_not_fixed())
 
     p2_1 = Population(10)
-    p2_1.print_ids()
-    p2_1.print_fitness()
+    print(p2_1.get_ids())
+    print(p2_1.get_fitnesses())
 
     for x in range(20):
         p2_1.next_genmo()
-        p2_1.print_ids()
-        p2_1.print_fitness()
+        print(p2_1.get_ids())
+    print(p2_1.get_fitnesses())
 
     p2_2 = Population(10, 0.3, 0.2)
-    p2_2.print_ids()
-    p2_2.print_fitness()
+    print(p2_2.get_ids())
+    print(p2_2.get_fitnesses())
 
     for x in range(20):
         p2_2.next_genmo()
-        p2_2.print_ids()
-    p2_2.print_fitness()
+        print(p2_2.get_ids())
+    print(p2_2.get_fitnesses())
 
 
 if __name__ == '__main__':

hamazaki1990/visualize.py

@@ -0,0 +1,38 @@
+import csv
+from population import Population
+
+
+def change_allelewf(population):
+    t = 0
+    fixprocess = [[t, population.get_mutantfreq()]]
+    while population.mutation_is_not_fixed():
+        t += 1
+        population.next_genwf()
+        fixprocess.append([t, population.get_mutantfreq()])
+    return fixprocess
+
+
+def change_allelemo(population):
+    t = 0
+    fixprocess = [[t, population.get_mutantfreq()]]
+    while population.mutation_is_not_fixed():
+        t += 1
+        population.next_genmo()
+        fixprocess.append([t, population.get_mutantfreq()])
+    return fixprocess
+
+
+def output_allelechange(filename, population, function):
+    with open(filename, "w", encoding="utf-8") as outfile:
+        writer = csv.writer(outfile)
+        writer.writerow(["generation", "derived_allele_frequency"])
+        fixprocess = function(population)
+        for x in range(len(fixprocess)):
+            writer.writerow(fixprocess[x])
+
+
+p1 = Population(10, 0.1, 0.2)
+output_allelechange("allelefreqwf.csv", p1, change_allelewf)
+
+p2 = Population(10, 0.1, 0.5)
+output_allelechange("allelefreqmo.csv", p2, change_allelemo)

hamazaki1990/visualize.r

@@ -0,0 +1,13 @@
+library("tidyverse")
+setwd("~/github/practice-py/hamazaki1990/")
+freq_wf <- read_csv("allelefreqwf.csv") %>%
+    dplyr::mutate(model = "wf")
+freq_wf
+freq_mo <- read_csv("allelefreqmo.csv") %>%
+    dplyr::mutate(model = "moran")
+freq_mo
+freq <- dplyr::bind_rows(freq_wf, freq_mo)
+print(freq)
+freqplot <- ggplot(freq, aes(x=generation, y=derived_allele_frequency, group=model, color=model))
+freqplot <-freqplot + geom_line()
+print(freqplot)