def plot_go_vs_p(list_name):
"""
A function to plot GO Term vs P-value with label of gene count on each bar
================================================
example:
>>>from intermine import query_manager as qm
>>>b.plot_go_vs_p("PL_obesityMonogen_ORahilly09")
"""
link = "http://registry.intermine.org/service/instances/" + mine
r = requests.get(link)
dict = json.loads(r.text)
url = dict["instance"]["url"]
service = Service(url)
lm = service.list_manager()
store = lm.get_list(name=list_name)
r = store.calculate_enrichment(widget="go_enrichment_for_gene")
gene_count = []
identifier = []
p_value = []
object_count = 0
for i in r:
if object_count < 5:
gene_count.append(i.matches)
identifier.append(i.identifier)
p_value.append(i.p_value)
object_count = object_count + 1
else:
if object_count >= 5:
break
y = pd.Series(p_value)
x = identifier
# Plot the figure.
ax = y.plot(kind='bar')
ax.set_title('GO Term vs p-value (Label: Gene count)')
ax.set_xlabel('GO Term')
ax.set_ylabel('p_value')
ax.set_xticklabels(x, rotation='horizontal')
rects = ax.patches
def autolabel(rects, ax):
i = 0
for rect in rects:
x = rect.get_x() + rect.get_width()/2.
y = rect.get_height()
ax.annotate(gene_count[i], (x, y), xytext=(0, 5),
textcoords="offset points",
ha='center', va='bottom')
i = i+1
autolabel(ax.patches, ax)
ax.margins(y=0.1)
plt.show()
def attack(self):
username = "******".format(self.ident)
password = "******"
try:
s = Service(self.service.root, username, password)
s.deregister(s.get_deregistration_token())
self.counter.add(3)
except:
pass
s = self.service.register(username, password)
self.LOG.debug("Registered user " + username)
self.counter.add(1)
c = 0
classes = s.model.classes.values()
self.counter.add(1)
classkeys = s._get_json('/classkeys')['classes']
self.counter.add(1)
while c == 0:
table = random.choice(classes)
if not (table.has_id and table.name in classkeys):
continue
query = s.query(table.name).select(classkeys[table.name][0])
c = query.count()
self.counter.add(1)
n = random.randint(1, min(100, c))
members = random.sample(map(lambda r: r[0], query.rows()), n)
self.counter.add(1)
self.LOG.debug("Will construct list of %s with: %r", table.name, members)
with s.list_manager() as lm:
l = lm.create_list(members, table.name)
self.LOG.debug('Created list %s, size: %d', l.name, l.size)
self.counter.add(1)
try:
s.deregister(s.get_deregistration_token())
self.counter.add(2)
except:
pass
def plot_go_vs_p(list_name):
"""
A function to plot GO Term vs P-value with label of gene count on each bar
================================================
example:
>>>from intermine import query_manager as qm
>>>b.plot_go_vs_p("PL_obesityMonogen_ORahilly09")
"""
link = "http://registry.intermine.org/service/instances/" + mine
r = requests.get(link)
dict = json.loads(r.text)
url = dict["instance"]["url"]
service = Service(url)
lm = service.list_manager()
store = lm.get_list(name=list_name)
r = store.calculate_enrichment(widget="go_enrichment_for_gene")
gene_count = []
identifier = []
p_value = []
object_count = 0
for i in r:
if object_count < 5:
gene_count.append(i.matches)
identifier.append(i.identifier)
p_value.append(i.p_value)
object_count = object_count + 1
else:
if object_count >= 5:
break
y = pd.Series(p_value)
x = identifier
# Plot the figure.
ax = y.plot(kind='bar')
ax.set_title('GO Term vs p-value (Label: Gene count)')
ax.set_xlabel('GO Term')
ax.set_ylabel('p_value')
ax.set_xticklabels(x, rotation='horizontal')
rects = ax.patches
def autolabel(rects, ax):
i = 0
for rect in rects:
x = rect.get_x() + rect.get_width() / 2.
y = rect.get_height()
ax.annotate(gene_count[i], (x, y),
xytext=(0, 5),
textcoords="offset points",
ha='center',
va='bottom')
i = i + 1
autolabel(ax.patches, ax)
ax.margins(y=0.1)
plt.show()
