def pipeline_degree(g, essential_proteins):
thresholds = (1, 2) # TODO
protein_count_total = [] # number of proteins with a degree >= threshold
protein_count_essential = [] # same for essential proteins
degrees = centrality_degree(g)
for threshold in thresholds:
protein_count_total.append(0)
protein_count_essential.append(0)
for vertex, degree in degrees:
if degree >= threshold:
if vertex.attributes()['name'] in essential_proteins:
protein_count_essential[-1] += 1
protein_count_total[-1] += 1
# plotting proportions
plot_stats(
protein_count_total,
protein_count_essential,
thresholds,
)
# hypergeometric test
pvalues = []
for index, threshold in enumerate(thresholds):
protein_count = len(g.vs)
# total number of protein: protein_count,
# subset of proteins: protein_count_total[index]
# total number of essential proteins: len(essential_proteins)
# number of essential proteins in subset: protein_count_essential[index]
pvalues.append(phyper(
protein_count, len(essential_proteins),
protein_count_total[index],
protein_count_essential[index]
))
# plotting p-value evolution
plot_phyper(pvalues, thresholds)
def plot_dumb_stats():
"""Show statistics about proteins awesomness"""
plot_stats(
(40, 23, 12), # all proteins
(20, 11, 7), # essential proteins
(1, 5, 10), # awesomness levels
stat_name='awesomness', #xlabels
all_color='magenta',
essential_color='yellow')
def plot_dumb_stats():
"""Show statistics about proteins awesomness"""
plot_stats(
(40, 23, 12), # all proteins
(20, 11, 7), # essential proteins
( 1, 5, 10), # awesomness levels
stat_name='awesomness', #xlabels
all_color='magenta',
essential_color='yellow'
)
def pipeline_degree(g, essential_proteins, centrality, thresholds):
# thresholds = (1, 2, 5, 8, 12, 20) # TODO
# thresholds = range(1, 20) # TODO
protein_count_total = [] # number of proteins with a degree >= threshold
protein_count_essential = [] # same for essential proteins
# degrees = centrality_degree(g)
degrees = [(v, centrality(v)) for v in g.vs]
for threshold in thresholds:
protein_count_total.append(0)
protein_count_essential.append(0)
for vertex, degree in degrees:
if degree >= threshold:
if vertex.attributes()['name'] in essential_proteins:
protein_count_essential[-1] += 1
protein_count_total[-1] += 1
# plotting proportions
plot_stats(
protein_count_total,
protein_count_essential,
thresholds,
)
# hypergeometric test
pvalues = []
for index, threshold in enumerate(thresholds):
protein_count = len(g.vs)
# total number of protein: protein_count,
# subset of proteins: protein_count_total[index]
# total number of essential proteins: len(essential_proteins)
# number of essential proteins in subset: protein_count_essential[index]
pvalues.append(phyper(
protein_count, len(essential_proteins),
protein_count_total[index],
protein_count_essential[index]
))
# plotting p-value evolution
plot_phyper(pvalues, thresholds)