def layout(node):
if node.is_leaf():
F = faces.PieChartFace([10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6],
colors=COLOR_SCHEMES["set3"],
width=50,
height=50)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
F = faces.PieChartFace([10, 20, 5, 5, 60],
colors=COLOR_SCHEMES[random.sample(
schema_names, 1)[0]],
width=100,
height=40)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
else:
F = faces.BarChartFace(
[40, 20, 70, 100, 30, 40, 50, 40, 70, -12],
min_value=-12,
colors=COLOR_SCHEMES["spectral"],
labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","))
faces.add_face_to_node(F, node, 0, position="branch-top")
F.background.color = "#eee"
def phyparts_pie_layout(mynode):
if mynode.name in phyparts_pies:
pie = faces.PieChartFace(
phyparts_pies[mynode.name],
#colors=COLOR_SCHEMES["set1"],
colors=["blue", "green", "red", "dark gray"],
width=50,
height=50)
pie.border.width = None
pie.opacity = 0.5
faces.add_face_to_node(pie, mynode, 0, position="branch-right")
concord_text = faces.TextFace(str(int(concord_dict[mynode.name])) +
' ',
fsize=20)
conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name])) +
' ',
fsize=20)
faces.add_face_to_node(concord_text, mynode, 0, position="branch-top")
faces.add_face_to_node(conflict_text,
mynode,
0,
position="branch-bottom")
else:
F = faces.TextFace(mynode.name, fsize=20)
faces.add_face_to_node(F, mynode, 0, position="aligned")
def layout(node):
if not node.is_leaf():
size = random.randint(20, 50)
F = faces.PieChartFace([10, 20, 60, 10],
colors=COLOR_SCHEMES[random.sample(
schema_names, 1)[0]],
width=size,
height=size)
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="float")
def layout(self, node):
scale=self.scaling
eps = .000000001
node_taxid = str(node.taxid)
if node_taxid in self.profile_tax_id_to_percentage and self.profile_tax_id_to_percentage[node_taxid]['percentage'] > 0.:
if (scale=="log"):
size_profile = (np.log(self.profile_tax_id_to_percentage[node_taxid]['percentage'])+9.)/11.*self.label_size
elif(scale=="sqrt"):
size_profile = (np.sqrt(self.profile_tax_id_to_percentage[node_taxid]['percentage'])-0.0000316227766)/10*self.label_size
elif(scale=="exponent"):
size_profile = (np.exp(self.profile_tax_id_to_percentage[node_taxid]['percentage'])-1.000000001)/np.exp(100)*self.label_size
elif(scale=="linear"):
size_profile = (self.profile_tax_id_to_percentage[node_taxid]['percentage'])/100*self.label_size
else:
size_profile = eps
if node_taxid in self.ground_truth_tax_id_to_percentage and self.ground_truth_tax_id_to_percentage[node_taxid]['percentage'] > 0.:
if (scale=="log"):
size_ground_truth = (np.log(self.ground_truth_tax_id_to_percentage[node_taxid]['percentage'])+9.)/11.*self.label_size
elif(scale=="sqrt"):
size_ground_truth = (np.sqrt(self.ground_truth_tax_id_to_percentage[node_taxid]['percentage'])-0.0000316227766)/10*self.label_size
elif(scale=="exponent"):
size_ground_truth = (np.exp(self.ground_truth_tax_id_to_percentage[node_taxid]['percentage'])-1.000000001)/np.exp(100)*self.label_size
elif(scale=="linear"):
size_ground_truth = (self.ground_truth_tax_id_to_percentage[node_taxid]['percentage'])/100*self.label_size
else:
size_ground_truth = eps
chart_sizes = np.array([size_profile, size_ground_truth])
if not np.sum(chart_sizes) == 0:
chart_sizes = 100 * (chart_sizes / np.sum(chart_sizes))
if(self.labels=="All"):
F2 = TextFace(abbreaviate_name(node.sci_name), tight_text=True, fsize=self.font_size) # use the scientific name
faces.add_face_to_node(F2, node, column=0, position="branch-right")
elif(self.labels=="Leaf"):
if node.is_leaf():
F2 = TextFace(abbreaviate_name(node.sci_name), tight_text=True, fsize=self.font_size) # use the scientific name
faces.add_face_to_node(F2, node, column=0, position="branch-right")
if(self.layt=="Pie"): # PIE CHART
size = max([size_profile, size_ground_truth])
F = faces.PieChartFace(chart_sizes,colors=['#1b9e77', '#d95f02'],width=size, height=size)
elif(self.layt=="Circle"): #TWO CIRCLES SIDE BY SIDE
F=faces.CircleFace(radius=size_profile, color="#1b9e77", style='circle', label=None)
F1=faces.CircleFace(radius=size_ground_truth, color="#d95f02", style='circle', label=None)
F1.border.width = None
F1.opacity = 0.6
faces.add_face_to_node(F1, node, 0, position="float-behind")
elif(self.layt=="Rectangle"): #TWO CIRCLES SIDE BY SIDE
F=faces.RectFace(width=size_profile, height=self.label_width, fgcolor="#1b9e77",bgcolor="#1b9e77", label=None)
F1=faces.RectFace(width=size_ground_truth, height=self.label_width, fgcolor="#d95f02",bgcolor="#d95f02", label=None)
F1.border.width = None
F1.opacity = 0.6
faces.add_face_to_node(F1, node, 0, position="float-behind")
faces.add_face_to_node(F, node, 0, position="float-behind")
F.border.width = None
F.opacity = 0.6
def layout(self, node):
#if not node.is_leaf():
scale=self.scaling
eps = .000000001
node_taxid = str(node.taxid)
if node_taxid in self.profile_tax_id_to_percentage and self.profile_tax_id_to_percentage[node_taxid] > 0.:
if (scale=="log"):
size_profile = np.log(self.profile_tax_id_to_percentage[node_taxid])
elif(scale=="sqrt"):
size_profile = np.sqrt(self.profile_tax_id_to_percentage[node_taxid])
elif(scale=="exponent"):
size_profile = np.exp(self.profile_tax_id_to_percentage[node_taxid])
elif(scale=="linear"):
size_profile = (self.profile_tax_id_to_percentage[node_taxid])
else:
size_profile = eps
if node_taxid in self.ground_truth_tax_id_to_percentage and self.ground_truth_tax_id_to_percentage[node_taxid] > 0.:
if (scale=="log"):
size_ground_truth = np.log(self.ground_truth_tax_id_to_percentage[node_taxid])
elif(scale=="sqrt"):
size_ground_truth = np.sqrt(self.ground_truth_tax_id_to_percentage[node_taxid])
elif(scale=="exponent"):
size_ground_truth = np.exp(self.ground_truth_tax_id_to_percentage[node_taxid])
elif(scale=="linear"):
size_ground_truth = (self.ground_truth_tax_id_to_percentage[node_taxid])
else:
size_ground_truth = eps
size = 25*max([size_ground_truth, size_profile])
chart_sizes = np.array([size_profile, size_ground_truth])
# print(np.sum(chart_sizes))
if not np.sum(chart_sizes) == 0:
chart_sizes = 100 * (chart_sizes / np.sum(chart_sizes))
if(self.labels=="All"):
F2 = TextFace(abbreaviate_name(node.sci_name), tight_text=True, fsize=20) # use the scientific name
faces.add_face_to_node(F2, node, column=0, position="branch-right")
elif(self.labels=="Leaf"):
if node.is_leaf():
F2 = TextFace(abbreaviate_name(node.sci_name), tight_text=True, fsize=20) # use the scientific name
faces.add_face_to_node(F2, node, column=0, position="branch-right")
# print(chart_sizes)
if(self.layt=="Pie"): # PIE CHART
F = faces.PieChartFace(chart_sizes,colors=['#1b9e77', '#d95f02'],width=size, height=size)
elif(self.layt=="Bar"):# BAR CHART
F = faces.BarChartFace(chart_sizes, deviations=None, labels=None, colors=['#1b9e77', '#d95f02'],width=50, height=50, label_fsize=0, scale_fsize=0)
#print(chart_sizes, node.sci_name)
elif(self.layt=="Circle"): #TWO CIRCLES SIDE BY SIDE
F=faces.CircleFace(radius=size_profile*10, color="#1b9e77", style='circle', label=None)
F1=faces.CircleFace(radius=size_ground_truth*10, color="#d95f02", style='circle', label=None)
F1.border.width = None
F1.opacity = 0.6
faces.add_face_to_node(F1, node, 0, position="float-behind")
elif(self.layt=="Rectangle"): #TWO CIRCLES SIDE BY SIDE
F=faces.RectFace(width=size_profile*40, height=40, fgcolor="#1b9e77",bgcolor="#1b9e77", label=None)
F1=faces.RectFace(width=size_ground_truth*40, height=40, fgcolor="#d95f02",bgcolor="#d95f02", label=None)
F1.border.width = None
F1.opacity = 0.6
faces.add_face_to_node(F1, node, 0, position="float-behind")
faces.add_face_to_node(F, node, 0, position="float-behind")
F.border.width = None
F.opacity = 0.6