def plotViolin(self,data,labels_to_plot='all',series='all',transformations=None,save=True):
if transformations is None:
transformations = [(lambda x: x,'')]
timestamp = utils.s_timestamp()
figure_folder = os.path.join(self._default_figure_folder,timestamp)
if save:
#create a separate_folder
if not os.path.exists(figure_folder):
os.makedirs(figure_folder)
if series == 'all':
series = data.keys()
if labels_to_plot == 'all':
labels_to_plot = data[series[0]].keys()
for label_to_plot in labels_to_plot:
plt.figure(figsize=(10,15))
data_to_plot = []
for transformation_fun,transformation_label in transformations:
for serie_name in series:
series_data = data[serie_name]
if label_to_plot not in series_data:
raise ValueError('Label "{0}" not in series "{1}"'.format(label_to_plot,serie_name))
raw_data = np.array([val for val in series_data[label_to_plot] if val is not None])
transformed_data = transformation_fun(raw_data)
data_to_plot.append(transformed_data)
plt.ylabel(label_to_plot)
plt.title(label_to_plot)
plt.violinplot(data_to_plot,showmedians=True)
plt.xticks( range(1,1+len(series)), series )
plt.ylim([min([qwe for asd in data_to_plot for qwe in asd])-3,max([qwe for asd in data_to_plot for qwe in asd])+3])
if save:
plt.savefig(os.path.join(figure_folder,self.getDescr(label_to_plot))+'.png')
else:
plt.show()
def plotHistogram(self,data,labels_to_plot='all',series='all',nbins=10,transformations=None,save=True,draw_normal=True,draw_bimodal=True):
if transformations is None:
transformations = [(lambda x: x,'')]
timestamp = utils.s_timestamp()
figure_folder = os.path.join(self._default_figure_folder,timestamp)
if save:
#create a separate_folder
if not os.path.exists(figure_folder):
os.makedirs(figure_folder)
if series == 'all':
series = data.keys()
if labels_to_plot == 'all':
labels_to_plot = data[series[0]].keys()
fitters_ = []
if draw_normal:
fitters_.append(fitters.NormalFitter)
if draw_bimodal:
fitters_.append(fitters.BiModalFitter)
for label_to_plot in labels_to_plot:
plt.figure(figsize=(10,15))
i = 1
for transformation_fun,transformation_label in transformations:
for serie_name in series:
plt.subplot(len(transformations),len(series),i)
i += 1
series_data = data[serie_name]
if label_to_plot not in series_data:
raise ValueError('Label "{0}" not in series "{1}"'.format(label_to_plot,serie_name))
raw_data = np.array([val for val in series_data[label_to_plot] if val is not None])
transformed_data = transformation_fun(raw_data)
title = transformation_label+' '+serie_name+' '
n, bins, patches = plt.hist(transformed_data, bins=nbins, normed=False)
data_pdf = n/sum(n)
bin_centers = [(bins[i_]+bins[i_+1])/2.0 for i_ in range(len(bins)-1)]
#plt.xlabel(transformation_label+' '+label_to_plot)
plt.ylabel('Count')
fitted = []
for fitter in fitters_:
temp = fitter(transformed_data)
fitted.append(temp)
p = temp.pdf(bin_centers)
plt.plot(bin_centers, p*sum(n), 'k', linewidth=2)
mse = (np.array(data_pdf-p)**2).mean()*100
#title += '\nmse {0}:{1:.2f}'.format(temp._descr,mse)
fitter_combinations = [(f1i,f2i) for f1i,f1 in enumerate(fitters_) for f2i,f2 in enumerate(fitters_) if f1i < f2i]
for f1i,f2i in fitter_combinations:
f1,f2 = fitted[f1i],fitted[f2i]
title += ' {0}vs{1}:{2:.2f}'.format(f1._descr,f2._descr,self.f_test(n/sum(n),f1.pdf(bin_centers),f2.pdf(bin_centers),f1._n_params,f2._n_params,len(transformed_data)))
plt.title(title)
if save:
plt.savefig(os.path.join(figure_folder,self.getDescr(label_to_plot))+'.png')
else:
plt.show()
def plotDiGraphViaGraphViz(n_nodes, ebunch, cmap, pos=None, node_labels=None):
def getForwardLinks():
return [(from_node, to_node) for from_node, to_node, _ in ebunch if from_node < to_node]
if node_labels is None:
node_labels = [str(i + 1) for i in range(n_nodes)]
file_ = os.path.join(PROJECT_DIR, 'output', 'temp', s_timestamp() + ".dot")
flag = ''
# flag = '\tsplines = true;\n'
if pos is None:
pos = _posTree(getForwardLinks())
flag = '\tsplines = true;\n'
with open(file_, 'w') as pout:
pout.write('digraph G {{\n'.format(n_nodes))
pout.write('\tsplines="curved";\n')
pout.write(flag)
pout.write('\tInput [pos="0,0!" color=white];\n')
for node_idx in range(n_nodes):
r, g, b, a = cmap(node_idx * 1.0 / n_nodes)
color = struct.pack('BBB', *(r * 255, g * 255, b * 255)).encode('hex')
pout.write(
'\t{0} [pos="{2},{3}!" shape=circle style=filled fillcolor="#{1}" width=.5 fixedsize=true];\n'.format(
node_labels[node_idx], color, pos[node_idx][0], pos[node_idx][1]))
for from_node, to_node, weight in ebunch:
color = "black"
extra = ""
if from_node > to_node:
extra = ''
if weight < 0:
color = "red"
extra += ' arrowhead="tee"'
else:
color = "green"
pout.write(
'\t{0} -> {1} [color="{2}" {3}];\n'.format(node_labels[from_node], node_labels[to_node], color, extra))
pout.write('\tInput -> {0} [color="black"];\n'.format(node_labels[0]))
pout.write('}\n')
out_file = file_ + ".png"
command = 'neato -Tpng "' + file_ + '" > "' + out_file
call(command, shell=True, env=os.environ)
img = -1
while 1:
try:
img = mpimg.imread(out_file)
break
except:
time.sleep(1)
print 'Sleep'
plt.imshow(img)
plt.axis('off')
return pos
def plotDiGraphViaGraphViz(n_nodes, ebunch, cmap, pos=None, node_labels=None):
def getForwardLinks():
return [(from_node, to_node) for from_node, to_node, _ in ebunch
if from_node < to_node]
if node_labels is None:
node_labels = [str(i + 1) for i in range(n_nodes)]
file_ = os.path.join(PROJECT_DIR, 'output', 'temp', s_timestamp() + ".dot")
#flag = ''
flag = '\tsplines = true; overlap=true\n'
if pos is None:
pos = _posTree(getForwardLinks())
flag = '\tsplines = true;\n'
with open(file_, 'w') as pout:
pout.write('digraph G {{\n'.format(n_nodes))
pout.write('\tsplines="curved";\n')
pout.write(flag)
pout.write('\tInput [pos="0,0!" color=white];\n')
for node_idx in range(n_nodes):
r, g, b, a = cmap(node_idx * 1.0 / n_nodes)
color = struct.pack('BBB',
*(r * 255, g * 255, b * 255)).encode('hex')
pout.write(
'\t{0} [pos="{2},{3}!" shape=circle style=filled fillcolor="#{1}" width=.5 fixedsize=true];\n'
.format(node_labels[node_idx], color, pos[node_idx][0],
pos[node_idx][1]))
for from_node, to_node, weight in ebunch:
color = "black"
extra = ""
if weight < 0:
color = "red"
extra += ' arrowhead="tee"'
pout.write('\t{0} -> {1} [color="{2}" {3}];\n'.format(
node_labels[from_node], node_labels[to_node], color, extra))
pout.write('\tInput -> {0} [color="black"];\n'.format(node_labels[0]))
pout.write('}\n')
out_file = file_ + ".png"
command = 'neato -Tpng "' + file_ + '" > "' + out_file
call(command, shell=True, env=os.environ)
img = -1
while 1:
try:
img = mpimg.imread(out_file)
break
except:
time.sleep(1)
print 'Sleep'
plt.imshow(img)
plt.axis('off')
return pos
def run(self, data, series, strains):
all_pairs = [(i1, i2) for i1, _ in enumerate(strains) for i2, _ in enumerate(strains) if i1 < i2]
with open(os.path.join(self._default_res_folder, utils.s_timestamp() + ".txt"), "w") as pout:
for series_name in series:
for i1, i2 in all_pairs:
strain1, strain2 = strains[i1], strains[i2]
data1, data2 = (
utils.removeNoneValues(data[strain1][series_name]),
utils.removeNoneValues(data[strain2][series_name]),
)
smallu, bigu, z, p = self.mannwhitneyu(data1, data2)
pout.write(
"Strain1: {0: <13} Strain2: {1: <13} Series: {2: <20} p: {3:8.5f}\n".format(
strain1, strain2, series_name, p
)
)
def plotDiGraphViaGraphVizASD(n_nodes,
ebunch,
cmap,
pos=None,
node_labels=None,
method_symmetrical=True):
file_ = os.path.join(PROJECT_DIR, 'output', 'temp', s_timestamp() + ".dot")
flag = '\tsplines = true;\n'
with open(file_, 'w') as pout:
pout.write('digraph G {{\n'.format(n_nodes))
pout.write('\tsplines="curved";\n')
pout.write(flag)
for node_idx in range(n_nodes):
r, g, b, a = cmap(node_idx * 1.0 / n_nodes)
color = struct.pack('BBB',
*(r * 255, g * 255, b * 255)).encode('hex')
pout.write(
'\t{0} [pos="{2},{3}!" shape=circle style=filled fillcolor="#{1}" width=.5 fixedsize=true];\n'
.format(node_labels[node_idx], color, pos[node_idx][0],
pos[node_idx][1]))
for from_node, to_node, weight in ebunch:
color = "black"
extra = ""
if weight < 0:
color = "red"
if not method_symmetrical:
extra += ' arrowhead="tee"'
if method_symmetrical:
extra += ' arrowhead="none"'
pout.write('\t{0} -> {1} [color="{2}" {3}];\n'.format(
node_labels[from_node], node_labels[to_node], color, extra))
pout.write('}\n')
out_file = file_ + ".png"
command = 'neato -Tpng "' + file_ + '" > "' + out_file
call(command, shell=True, env=os.environ)
return pos
