def graphNumberOfProteinPerGeneration(proteins_per_generation):
from drawSVGGraph import Graph
num_proteins_per_generation = [
len(proteins) for proteins in proteins_per_generation
]
g = Graph()
g.addData({'proteins': num_proteins_per_generation})
g.x_gridlines = False
g.plot()
g.write('test_graph')
def graphNumberOfProteinPerGeneration(proteins_per_generation):
from drawSVGGraph import Graph
num_proteins_per_generation = [len(proteins)for proteins in proteins_per_generation]
g = Graph()
g.addData({'proteins': num_proteins_per_generation})
g.x_gridlines = False
g.plot()
g.write('test_graph')
def plotFitness(fitnesses):
from drawSVGGraph import Graph
g = Graph({'height': 200, 'width': 500})
g.addData({
'max': [f[0] for f in fitnesses],
'median': [f[63] for f in fitnesses]
})
g.x_gridlines = False
g.colours = ['#3C9DD0', '#034569', '#0C0874']
g.addStyle('.gridlines', {'opacity': 0.2})
g.x_axis_label = "Generations"
g.y_axis_label = "Concentration of IH"
g.div_x = 480
g.plot()
g.write('Fitness over generations')
def plotMetabolites():
# Get metabolites from file of just metabolites
filename = os.path.join("Genomes", "Gen 1920 metabolites.txt")
metabolites_per_generation = []
with open(filename, 'r') as fin:
for line in fin:
d = {}
for metabolites in line.split(', '):
m, v = metabolites.split(':')
d[m] = float(v)
metabolites_per_generation.append(d)
# Only look at the first 1000 generations
metabolites_per_generation = metabolites_per_generation[:1000]
def getMetabolite(m):
""" Get list of concentrations over the generations for a given metabolite.
Return as a percentage of the initial concentration and bin into bins of 5. """
initial_concentration = metabolites_per_generation[0][m]
return [
1000 * (generation[m] - initial_concentration)
for generation in metabolites_per_generation
]
metabolites_of_interest = ['K', 'F', 'G']
metabolites_of_interest = ['E', 'H', 'I']
metabolites_of_interest = ['IL', 'FG', 'FK']
metabolites_of_interest = ['E', 'H', 'I', 'IL', 'K', 'F', 'G', 'FG', 'FK']
metabolite_data = {
metabolite: getMetabolite(metabolite)
for metabolite in metabolites_of_interest
}
for m in metabolites_of_interest:
print m, metabolite_data[m][-1]
from drawSVGGraph import Graph
g = Graph({'height': 300, 'width': 450})
g.addData(metabolite_data)
g.x_gridlines = False
g.colours = ['#3C9DD0', '#034569', '#0C0874']
g.colours = ['#111'] * 9
g.addStyle('.gridlines', {'opacity': 0.2})
g.x_axis_label = "Generations"
g.y_axis_label = "Change in concentration"
#g.min_y = 0
g.plot()
g.write('Conc of E over generations')
def plotFitness(fitnesses):
from drawSVGGraph import Graph
g = Graph({'height': 200, 'width': 500})
g.addData({'max': [f[0] for f in fitnesses], 'median': [f[63] for f in fitnesses]})
g.x_gridlines = False
g.colours = ['#3C9DD0', '#034569', '#0C0874']
g.addStyle('.gridlines', {'opacity':0.2})
g.x_axis_label = "Generations"
g.y_axis_label = "Concentration of IH"
g.div_x = 480
g.plot()
g.write('Fitness over generations')
def plotMetabolites():
# Get metabolites from file of just metabolites
filename = os.path.join("Genomes", "Gen 1920 metabolites.txt")
metabolites_per_generation = []
with open(filename, 'r') as fin:
for line in fin:
d = {}
for metabolites in line.split(', '):
m, v = metabolites.split(':')
d[m] = float(v)
metabolites_per_generation.append(d)
# Only look at the first 1000 generations
metabolites_per_generation = metabolites_per_generation[:1000]
def getMetabolite(m):
""" Get list of concentrations over the generations for a given metabolite.
Return as a percentage of the initial concentration and bin into bins of 5. """
initial_concentration = metabolites_per_generation[0][m]
return [1000 * (generation[m] - initial_concentration) for generation in metabolites_per_generation]
metabolites_of_interest = ['K', 'F', 'G']
metabolites_of_interest = ['E', 'H', 'I']
metabolites_of_interest = ['IL', 'FG', 'FK']
metabolites_of_interest = ['E', 'H', 'I', 'IL', 'K', 'F', 'G', 'FG', 'FK']
metabolite_data = {metabolite: getMetabolite(metabolite) for metabolite in metabolites_of_interest}
for m in metabolites_of_interest:
print m, metabolite_data[m][-1]
from drawSVGGraph import Graph
g = Graph({'height': 300, 'width': 450})
g.addData(metabolite_data)
g.x_gridlines = False
g.colours = ['#3C9DD0', '#034569', '#0C0874']
g.colours = ['#111'] * 9
g.addStyle('.gridlines', {'opacity':0.2})
g.x_axis_label = "Generations"
g.y_axis_label = "Change in concentration"
#g.min_y = 0
g.plot()
g.write('Conc of E over generations')