solved heavywatal#20

hamazaki1990/population.py

@@ -23,6 +23,11 @@ def get_fitnesses(self):
         fitness = [x.get_fitness() for x in self._inds]
         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]
         size = len(self._inds)
@@ -74,6 +79,7 @@ def main():
     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()

hamazaki1990/visualize.py

@@ -1,35 +1,39 @@
 import csv
-import pandas as pd
 from population import Population
 
 
 def change_allelewf(population):
-    fit_list = population.get_fitnesses()
-    fixprocess = [1 - fit_list.count(1.0)/len(fit_list)]
+    t = 0
+    fixprocess = [[t, population.get_mutantfreq()]]
     while population.mutation_is_not_fixed():
+        t += 1
         population.next_genwf()
-        fit_list = population.get_fitnesses()
-        mutantrate = 1 - fit_list.count(1.0)/len(fit_list)
-        fixprocess.append(mutantrate)
+        fixprocess.append([t, population.get_mutantfreq()])
     return fixprocess
 
 
 def change_allelemo(population):
-    fit_list = population.get_fitnesses()
-    fixprocess = [1 - fit_list.count(1.0)/len(fit_list)]
+    t = 0
+    fixprocess = [[t, population.get_mutantfreq()]]
     while population.mutation_is_not_fixed():
+        t += 1
         population.next_genmo()
-        fit_list = population.get_fitnesses()
-        mutantrate = 1 - fit_list.count(1.0)/len(fit_list)
-        fixprocess.append(mutantrate)
+        fixprocess.append([t, population.get_mutantfreq()])
     return fixprocess
 
 
 csvfile1 = open("allelechangewf.csv", "w", encoding="utf-8")
 writer = csv.writer(csvfile1)
 p1 = Population(10, 0.1, 0.5)
-writer.writerow(change_allelewf(p1))
+fixprocesswf = change_allelewf(p1)
+writer.writerow(["generation", "derived_allele_frequency"])
+for x in range(len(fixprocesswf)):
+    writer.writerow(fixprocesswf[x])
 
-
-p2 = Population(10, 0.1, 0.5)
-print(change_allelemo(p2))
+csvfile2 = open("allelechangemo.csv", "w", encoding="utf-8")
+writer = csv.writer(csvfile2)
+p1 = Population(10, 0.1, 0.5)
+fixprocessmo = change_allelemo(p1)
+writer.writerow(["generation", "derived_allele_frequency"])
+for x in range(len(fixprocessmo)):
+    writer.writerow(fixprocessmo[x])

hamazaki1990/visualize.r

@@ -1,7 +1,12 @@
-install.packages("tidyverse")
 library("tidyverse")
-allelefreq=read_csv("~/github/practice-py/hamazaki1990/allelechangewf.csv", col_names = FALSE)
-names(allelefreq)=c("generation","derived_allele_frequency")
-freqprot=ggplot(allelefreq, x=generation, y=derived_allele_frequency)
-freqprot=freqprot+geom_line()
-print(freqprot)
+freq <- read_csv("~/github/practice-py/hamazaki1990/allelechangewf.csv")
+freq
+freqplot <- ggplot(freq, aes(x = generation, y = derived_allele_frequency))
+freqplot <- freqplot + geom_line()
+print(freqplot)
+
+freq1 <- read_csv("~/github/practice-py/hamazaki1990/allelechangemo.csv")
+freq1
+freqplot1 <- ggplot(freq1, aes(x = generation, y = derived_allele_frequency))
+freqplot1 <- freqplot1 + geom_path(size=2, linetype="dashed")
+print(freqplot1)