def plot_cotrans_counts():
run_data = spats_run_data()
plt.xlim([run_data.min_length, run_data.n + 1]) # Change x-axis here
plt.plot(run_data.all_sites, run_data.total_treated_counts, color = colors.red, label = '(+)')
plt.plot(run_data.all_sites, run_data.total_untreated_counts, color = colors.blue, label = '(-)')
plt.title("Total Treated/Untreated Counts")
plt.xlabel("RNA Length")
plt.ylabel("# of Stops")
plt.legend()
return plt
def plot_cotrans_c():
run_data = spats_run_data()
plt.xlim([run_data.min_length, run_data.n + 1]) #Change x-axis here
plt.plot(run_data.all_sites, run_data.c_values, color = colors.black, label = "c")
plt.plot(run_data.all_sites, [0.4 for i in run_data.all_sites], color = colors.red, label = "Recommended Cutoff")
ax = plt.gca(); ax.yaxis.grid(True)
plt.title("c Values")
plt.xlabel("RNA Length")
plt.ylabel("c")
plt.legend()
return plt
def plot_sl_counts(path = None):
run_data = spats_run_data(path)
row = run_data.single_profile
plt.xlim([0, run_data.n + 1])
plt.plot(row.x_axis, row.treated, color = colors.red, label = 'f+')
plt.plot(row.x_axis, row.untreated, color = colors.blue, label = 'f-')
plt.title("Total Treated/Untreated Counts")
plt.xlabel("Site")
plt.ylabel("# of Stops")
plt.legend()
return plt
def plot_reactivity(reactivity_type):
run_data = spats_run_data()
row = run_data.single_profile
reactivity = getattr(row, reactivity_type)
plt.xlim([0, run_data.n + 1])
plt.ylim([0, max(reactivity)])
plt.plot(row.x_axis, reactivity, 1, label=reactivity_type)
#plt.bar(row.x_axis, reactivity, 1, label=reactivity_type)
plt.xlabel("Nucleotide Position (nt)")
plt.ylabel(reactivity_type)
plt.legend()
return plt
def plot_sl_muts():
run_data = spats_run_data()
row = run_data.single_profile
plt.xlim([0, run_data.n + 1])
#plt.plot(row.x_axis, row.treated_counts, color = "red", label = 's+')
#plt.plot(row.x_axis, row.untreated_counts, color = "blue", label = 's-')
plt.plot(row.x_axis, row.treated_muts, color = "orange", label = 'mut+')
plt.plot(row.x_axis, row.untreated_muts, color = "purple", label = 'mut-')
plt.title("Total Treated/Untreated Mutations")
plt.xlabel("Site")
plt.ylabel("# of Mutations")
plt.legend()
return plt