def my_layout(node):
from ete2 import AttrFace, faces
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0, position="aligned")
else:
node.img_style["size"] = 0
node.img_style["fgcolor"] = "#000000"
def my_layout(node):
if node.is_leaf():
name_face = AttrFace("name",fsize=25)
faces.add_face_to_node(name_face, node, column=0, position="branch-right")
else:
name_face = AttrFace("name", fsize=20, fgcolor="red")
faces.add_face_to_node(name_face, node, column=0, position="branch-right")
def ultrametric_layout(node):
# node balls consume space in the tree picture, so partitions with
# many splits are not well aligned with partitions having less
# splits. To solve it, I set node sphere size to 0
node.img_style["size"] = 0
if node.is_leaf():
faces.add_face_to_node(nameFace, node, 0)
def makeSupportSymbols(node, secondary_support):
#function to make circle with size scaled to base support value and color of circle scaled to the level of the second support value
opacity = 0.01
# Let's make the sphere transparent
if secondary_support == None:
circle_color = "Grey"
opacity = 1.0
factor = 6
elif secondary_support >=95.0:
circle_color = "Black"
opacity = 1.0
factor = 10
elif secondary_support >=70.0:
circle_color = "Black"
opacity = 1.0
factor = 8
elif secondary_support <70.0:
circle_color = "Black"
opacity = 1.0
factor = 6
else:
print "secondary value unexpected: {}".format(secondary_support())
circle_color = "Red"
opacity = 1.0
#circle_color = "#33343E" #a black from the pomacanthus drawing
#print "color is {}, bootstrap is {}, opacity is {}".format(color, secondary_support, opacity)
support_face = CircleFace(radius=node.support * factor, color=circle_color, style="circle")
support_face.opacity = opacity
faces.add_face_to_node(support_face, node, 0, position="float-behind")
def ultrametric_layout(node):
# node balls consume space in the tree picture, so partitions with
# many splits are not well aligned with partitions having less
# splits. To solve it, I set node sphere size to 0
node.img_style["size"] = 0
if node.is_leaf():
faces.add_face_to_node(nameFace, node, 0)
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=7)
faces.add_face_to_node(faces.AttrFace("name", "Arial", 10, None),
node,
0,
position='branch-right')
def layout_simple(node):
if node.is_leaf():
attr = AttrFace("name",
fsize=10,
fgcolor="black",
text_prefix=" ",
fstyle="italic")
faces.add_face_to_node(attr, node, 0, position="aligned")
def master_ly(node):
if node.is_leaf():
# Create an ItemFAce. First argument must be the pointer to
# the constructor function that returns a QGraphicsItem. It
# will be used to draw the Face. Next arguments are arbitrary,
# and they will be forwarded to the constructor Face function.
F = faces.DynamicItemFace(ugly_name_face, 100, 50)
faces.add_face_to_node(F, node, 0, position="aligned")
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
small_tree = small_d[node.name]
T = TreeFace(small_tree,small_ts)
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def my_layout(node):
if node.is_leaf():
# If terminal node, draws its name
name_faces = AttrFace("name")
else:
# If internal node, draws label with smaller font size
name_faces = AttrFace("name", fsize=10)
# Adds the name face to the image at the preferred position
faces.add_face_to_node(name_faces, node, column=0, position="branch-right")
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(node):
if node.is_leaf():
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
small_tree = small_d[node.name]
T = TreeFace(small_tree, small_ts)
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def layout(node): if node.name in ckm_name_to_perc: ckm_perc = float(ckm_name_to_perc[node.name]) else: ckm_perc = 0 F = CircleFace(radius=3.14*math.sqrt(ckm_perc), color="RoyalBlue", style="sphere") F.border.width = None F.opacity = 0.6 faces.add_face_to_node(F,node, 0, position="branch-right") if label_internal_nodes: faces.add_face_to_node(TextFace(node.name, fsize=7),node, 0, position="branch-top")
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
global CONT
if CONT >= len(chars):
CONT = 0
if node.is_leaf():
node.img_style["size"] = 0
F2= AttrFace("name", tight_text=True)
F= TextFace(chars[CONT], tight_text=True)
F.inner_border.width = 0
F2.inner_border.width = 0
#faces.add_face_to_node(F ,node, 0, position="branch-right")
faces.add_face_to_node(F2 ,node, 1, position="branch-right")
CONT += 1
def test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout(node): if not node.is_root(): # give node name to all but the root faces.add_face_to_node(TextFace(node.name), node, 0) # and increase them with the wight if "weight" in node.features: # Creates a sphere face whose size is proportional to node's # feature "weight" C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere") # Let's make the sphere transparent C.opacity = 0.34 # And place as a float face over the tree faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
t = Tree()
t.populate(10)
T = TreeFace(t, small_ts)
# Let's make the sphere transparent
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def layout(node): if not node.is_root(): # give node name to all but the root faces.add_face_to_node(TextFace(node.name), node, 0) # and increase them with the wight if "weight" in node.features: # Creates a sphere face whose size is proportional to node's # feature "weight" C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere") # Let's make the sphere transparent C.opacity = 0.34 # And place as a float face over the tree faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
#print(node)
if node.is_leaf():
if node.name in x_file_names:
#make reconstructed bubble
size = x[x_file_names.index(node.name)]
F = CircleFace(radius=500*math.sqrt(size), color="RoyalBlue", style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="branch-right")
if taxonomic_names_on_leaves:
nameFace = AttrFace("name", fsize=25, fgcolor='black',text_suffix="_"+taxonomy[x_file_names.index(node.name)])
faces.add_face_to_node(nameFace, node, 0, position="branch-right")
else:
nameFace = AttrFace("name", fsize=25, fgcolor='black')
faces.add_face_to_node(nameFace, node, 0, position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in x_file_names:
idx = hyp_node_names[node.name][2]
size = x[x_file_names.index(node_base_name)+(idx+1)*len(x_file_names)]
F = CircleFace(radius=500*math.sqrt(size), color="RoyalBlue", style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="branch-right")
#print node
#print size
else:
size=0
else:
size=0
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
faces.add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=0
faces.add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
# If silhouette is good, creates a green bubble
if node.silhouette>0:
validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#056600")
node.img_style["fgcolor"]="#056600"
# Otherwise, use red bubbles
else:
validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#940000")
node.img_style["fgcolor"]="#940000"
# Sets node size proportional to the silhouette value.
node.img_style["shape"]="sphere"
if node.silhouette<=1 and node.silhouette>=-1:
node.img_style["size"]= 15+int((abs(node.silhouette)*10)**2)
# If node is very internal, draw also a bar diagram
# with the average expression of the partition
faces.add_face_to_node(validationFace, node, 0)
if len(node)>100:
faces.add_face_to_node(cbarsFace, node, 1)
def test_layout_phylo_aa_motif(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "aa",
fsize=10,special_col=special_col,
alt_col_w=3,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout(node):
if not node.is_root():
# Add node name to laef nodes
#N = AttrFace("name", fsize=14, fgcolor="black")
#faces.add_face_to_node(N, node, 0)
#pass
faces.add_face_to_node(TextFace(node.name), node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def layout2(node):
#node.img_style["size"] = random.randint(40, 200)
if hasattr(node, "size"):
f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
faces.add_face_to_node(f, node, 0, position="branch-top")
faces.add_face_to_node(f, node, 0, position="branch-bottom")
#f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
node.img_style["size"] = 10
node.img_style["shape"] = "square"
node.img_style["bgcolor"] = random_color()
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
def layout2(node):
#node.img_style["size"] = random.randint(40, 200)
if hasattr(node, "size"):
f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
faces.add_face_to_node(f, node, 0, position="branch-top")
faces.add_face_to_node(f, node, 0, position="branch-bottom")
#f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
node.img_style["size"] = 10
node.img_style["shape"] = "square"
node.img_style["bgcolor"] = random_color()
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
def layout(node):
node.img_style["size"] = random.randint(5,100)
node.img_style["hz_line_width"] = 5
node.img_style["vt_line_width"] = 10
if node.is_leaf():
#node.img_style["size"] = random.randint(50, 50)
f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
#f = faces.AttrFace("name", fsize=random.randint(20,20))
faces.add_face_to_node(f, node, 0, position="aligned")
f.border.width = 0
#f = faces.CircleFace(20, "red")
#f = faces.AttrFace("name", fsize=20)
f = faces.TextFace("NAME", fsize=10)
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
def layout(node):
def color(node):
if type(node.item) is Value:
return "Red"
elif type(node.item) is Parameter:
return "Yellow"
elif node.item.leaf:
return "Green"
else:
return "RoyalBlue"
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
C = CircleFace(radius=node.weight, color=color(node), style="sphere")
C.opacity = 0.3
faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
if node.is_leaf():
try:
sane_node_name = sanitize(node.name)
node.img_style['size'] = 10
longNameFace = faces.TextFace(node.name.ljust(MAX_LN_LEN),
ftype='courier',
fsize=12)
if node.name == 'Family Name':
for family in globalInfo.families:
tmp_png = globalInfo.gen_png('fam_name', family, angle=90, save=False)
faces.add_face_to_node(faces.ImgFace(tmp_png),
node, globalInfo.families.index(family)+2,
aligned = True)
else:
organism = globalInfo.results_data[sane_node_name]
print organism
for family in globalInfo.families:
if family in organism.keys():
num_other = 0
for label in organism[family]:
print 'candidate :', organism[family][label], globalInfo.families.index(family), len(organism[family][label])
if label in globalInfo.img.keys():
tmp_png = globalInfo.gen_png(label,
len(organism[family][label]))
faces.add_face_to_node(faces.ImgFace(tmp_png),
node, globalInfo.families.index(family)+2,
aligned = True)
else:
num_other += 1
if num_other:
tmp_png = globalInfo.gen_png('unknown', num_other)
faces.add_face_to_node(faces.ImgFace(tmp_png),
node, globalInfo.families.index(family)+2,
aligned = True)
else:
tmp_png = globalInfo.gen_png('nan', '')
faces.add_face_to_node(faces.ImgFace(tmp_png),
node, globalInfo.families.index(family)+2,
aligned = True)
faces.add_face_to_node(longNameFace, node, column=1, aligned=True)
except Exception, e:
print e
print traceback.print_exc()
def layout(node):
#if node.up is not None:
#attr = AttrFace("decrease", fsize=7, fgcolor="red", text_prefix="-")
#faces.add_face_to_node(attr, node, 0, position="branch-bottom")
if node.is_leaf():
attr = AttrFace("name",
fsize=10,
fgcolor="black",
text_prefix=" ",
fstyle="italic")
faces.add_face_to_node(attr, node, 0, position="aligned")
attr = AttrFace(args.feature_name,
fsize=7,
fgcolor="green",
text_prefix="")
faces.add_face_to_node(attr, node, 0, position="branch-top")
def aligned_faces(node):
if node.is_leaf():
for i in xrange(3):
F = faces.TextFace("ABCDEFGHIJK"[0:random.randint(1,11)])
F.border.width = 1
F.border.line_style = 1
F.inner_background.color = "lightgreen"
F.border.width = 1
F.inner_border.width = 1
F.background.color = "darkgreen"
F.border.width = 2
F.vt_align = random.randint(0,4)
F.hz_align = random.randint(0,4)
F.margin_bottom = random.randint(1, 20)
F.margin_right = random.randint(1, 20)
F.margin_left = random.randint(1, 20)
F.margin_top = random.randint(1, 20)
faces.add_face_to_node(F, node, i, position="aligned")
if random.randint(0, 1):
faces.add_face_to_node(F, node, i, position="aligned")
def layout(node):
node_style = NodeStyle()
node_style["hz_line_width"] = 10
node_style["vt_line_width"] = 10
node.set_style(node_style)
#print(node)
if node.is_leaf():
if node.name in org_names:
#make reconstructed bubble
size = x[org_names.index(node.name)]
F = CircleFace(radius=size_factor*math.sqrt(size), color="RoyalBlue", style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="branch-right")
#Denote that this was a training organism
nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
faces.add_face_to_node(nameFace, node, 0, position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in org_names:
idx = hyp_node_names[node.name][2]
size = x[org_names.index(node_base_name)+(idx+1)*len(org_names)]
F = CircleFace(radius=size_factor*math.sqrt(size), color="RoyalBlue", style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="branch-right")
#This is if I want the names of the hypothetical nodes to be printed as well
#nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
#faces.add_face_to_node(nameFace, node, 0, position="branch-right")
else:
size=0
else:
size=0
def my_layout(node):
if node.name != "43":
print node.name
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("species", fsize=16)
pie = PieChartFace([changes[node.name][0], changes[node.name][1]],
changes[node.name][2], changes[node.name][2],
["Green", "Red"])
pie.opacity = 0.5
#name_face = AttrFace("name", fsize=16)
faces.add_face_to_node(name_face,
node,
column=0,
position="branch-right")
faces.add_face_to_node(pie, node, column=0, position="float")
else:
# If internal node, draws label with smaller font size
#name_face = AttrFace("name", fsize=10)
pie = PieChartFace([changes[node.name][0], changes[node.name][1]],
changes[node.name][2], changes[node.name][2],
["Green", "Red"])
pie.opacity = 0.5
#faces.add_face_to_node(name_face, node, column=0, position="branch-right")
faces.add_face_to_node(pie, node, column=0, position="float")
def layout(node):
#print(node)
if node.is_leaf():
if node.name in x_file_names:
#make reconstructed bubble
size = x[x_file_names.index(node.name)]
F = CircleFace(radius=500 * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
if taxonomic_names_on_leaves:
nameFace = AttrFace(
"name",
fsize=25,
fgcolor='black',
text_suffix="_" +
taxonomy[x_file_names.index(node.name)])
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
else:
nameFace = AttrFace("name", fsize=25, fgcolor='black')
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in x_file_names:
idx = hyp_node_names[node.name][2]
size = x[x_file_names.index(node_base_name) +
(idx + 1) * len(x_file_names)]
F = CircleFace(radius=500 * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#print node
#print size
else:
size = 0
else:
size = 0
def tree_layout(node):
if not node.is_leaf():
#faces.add_face_to_node(AttrFace("mylabel"), node, column=1, position="branch-top")
faces.add_face_to_node(AttrFace("mylabel"), node, column=1)
else:
if hasattr(node,'color'):
faces.add_face_to_node(AttrFace("name",fgcolor=node.color), node, column=1)
else:
faces.add_face_to_node(AttrFace("name"), node, column=1)
def layout(node):
if node.is_leaf():
#######################################################
#~ Taxon Label Size and Margin Adjustment
N = AttrFace("name", fsize=1200, fgcolor="#000000")
N.margin_top = 250
N.margin_right = 100 #outside
N.margin_left = 1000 #inside
N.margin_bottom = 250
#######################################################
#######################################################
#~ Taxon Label Background Color Setting
tmp = "<myTaxaonLabel>"
#~ if not(node.name.find(tmp)) : N.background.color="#FF9999"
#######################################################
faces.add_face_to_node(N, node, 0, position="aligned")
if (not node.is_leaf()):
S = faces.AttrFace("support", fsize=200, fgcolor="#000000")
S.margin_top = 20
S.margin_right = 10
S.margin_left = 20
S.margin_bottom = 20
faces.add_face_to_node(S, node, column=0, position="float")
if "support" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.support * 20,
color="RoyalBlue",
style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, position="float", column=1)
style = NodeStyle()
style["size"] = 0
style["vt_line_width"] = 150
style["hz_line_width"] = 150
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
bgcol1 = "#FFCCCC"
bgcol2 = "#FFE5CC"
bgcol3 = "#FFFFCC"
bgcol4 = "#E5FFCC"
bgcol5 = "#CCFFCC"
bgcol6 = "#CCFFE5"
bgcol7 = "#FFCCE5"
bgcol8 = "#CCFFFF"
bgcol9 = "#CCE5FF"
bgcol10 = "#CCCCFF"
bgcol11 = "#E5CCFF"
def layout(node):
if node.is_leaf():
#######################################################
#~ Taxon Label Size and Margin Adjustment
N = AttrFace("name", fsize=1200,fgcolor="#000000")
N.margin_top = 250
N.margin_right = 100 #outside
N.margin_left = 1000 #inside
N.margin_bottom = 250
#######################################################
#######################################################
#~ Taxon Label Background Color Setting
tmp = "<myTaxaonLabel>"
#~ if not(node.name.find(tmp)) : N.background.color="#FF9999"
#######################################################
faces.add_face_to_node(N, node, 0, position="aligned")
if (not node.is_leaf()) :
S=faces.AttrFace("support", fsize=200, fgcolor="#000000")
S.margin_top = 20
S.margin_right = 10
S.margin_left = 20
S.margin_bottom = 20
faces.add_face_to_node( S, node, column=0 , position = "float")
if "support" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.support*20, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, position="float",column=1)
style = NodeStyle()
style["size"] = 0
style["vt_line_width"] = 150
style["hz_line_width"] = 150
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
bgcol1="#FFCCCC"
bgcol2="#FFE5CC"
bgcol3="#FFFFCC"
bgcol4="#E5FFCC"
bgcol5="#CCFFCC"
bgcol6="#CCFFE5"
bgcol7="#FFCCE5"
bgcol8="#CCFFFF"
bgcol9="#CCE5FF"
bgcol10="#CCCCFF"
bgcol11="#E5CCFF"
def calibrations_layout(node):
#width is set to 2 to increase visibility in large trees when exporting
node.img_style["hz_line_width"]=4
node.img_style["vt_line_width"]=4
if node.is_leaf():
node.img_style["size"] = 0
color = "#000000" # these two lines hide the default node symbol for tips. They are replaced by the textface below
faces.add_face_to_node( faces.TextFace(node.name, ftype="Arial", fsize=20, fstyle = "italic", fgcolor=color), node, 0 )
#try adding the family to the tip as well
#if node.name in ranks: # note that ranks is a dictionary that has not been passed in to the function. Could be trouble!
#family = ranks[node.name]
#faces.add_face_to_node( faces.TextFace(family, ftype="Arial", fsize=12, fgcolor="red"), node, 0 )
if node.up is None:
node.img_style["size"]=0
node.dist = 0.35 # you may need to change this value to fit the aspect of your tree
node.img_style["hz_line_color"] = "#ffffff"
if UNROOTED:
node.img_style["vt_line_type"] = 0.001
#add faces to nodes that have images. face_dict is defined outside this function too....
#if node.name in face_dict:
#faces.add_face_to_node(face_dict[node.name], node, column = 1, position = "branch-right")
#If node is an internal node
else:
#color the node if is is a major clade
#if node.nodeid in BG_COLORS:
#node.img_style["bgcolor"] = BG_COLORS[str(node.nodeid)]
# Sets the style of internal nodes
node.img_style["size"] = 0
#node.img_style["shape"] = "circle"
#node.img_style["fgcolor"] = "#000000"
#label internal nodes with nodenumber
num = node.nodenumber
faces.add_face_to_node(faces.TextFace(num, ftype="Arial", fsize=16, fgcolor="purple"), node, 0, position = "branch-right")
# add paml calibrations
if "paml_cal" in node.features:
faces.add_face_to_node(faces.TextFace(node.paml_cal, ftype="Arial", fsize=16, fgcolor="black"), node, 0, position = "branch-right")
if "raw_cal" in node.features:
faces.add_face_to_node(faces.TextFace(node.raw_cal, ftype="Arial", fsize=16, fgcolor="orange"), node, 0, position = "branch-right")
def layout(node):
if node.up is not None:
attr = AttrFace("significant_expansion",
fsize=7,
fgcolor="green",
text_prefix="+")
faces.add_face_to_node(attr, node, 0, position="branch-top")
attr = AttrFace("significant_contraction",
fsize=7,
fgcolor="red",
text_prefix="-")
faces.add_face_to_node(attr, node, 0, position="branch-bottom")
if node.is_leaf():
attr = AttrFace("name",
fsize=10,
fgcolor="black",
text_prefix=" ",
fstyle="italic")
faces.add_face_to_node(attr, node, 0, position="aligned")
def layout(node):
node_style = NodeStyle()
node_style["hz_line_width"] = 10
node_style["vt_line_width"] = 10
node.set_style(node_style)
#print(node)
if node.is_leaf():
if node.name in org_names:
#make reconstructed bubble
size = x[org_names.index(node.name)]
F = CircleFace(radius=size_factor * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#Denote that this was a training organism
nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in org_names:
idx = hyp_node_names[node.name][2]
size = x[org_names.index(node_base_name) +
(idx + 1) * len(org_names)]
F = CircleFace(radius=size_factor * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#This is if I want the names of the hypothetical nodes to be printed as well
#nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
#faces.add_face_to_node(nameFace, node, 0, position="branch-right")
else:
size = 0
else:
size = 0
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=20, fgcolor="black")
faces.add_face_to_node(N, node, 0)
elif "pie_data" in node.features:
# Creates a pie chart face whose size is proportional to node's
percents=node.pie_data
rcolor=[]
for i in xrange(0, len(percents)):
r= lambda: random.randint(0,255)
rcolor.append( ('#%02X%02X%02X' % (r(),r(),r())))
C = BarChartFace(percents, width=WIDTH, height=HEIGHT, colors=rcolor, min_value=0, max_value=100)
# Let's make the Bar Chart transparent
#C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, column=0, position="branch-top")
nameFace= AttrFace("name", fsize=20)
faces.add_face_to_node(nameFace, node, column=0, position="branch-bottom")
def __layout__(self, node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
nstyle = NodeStyle()
nstyle["size"] = 0
node.set_style(nstyle)
if "internalCount" in node.features:
print node.name
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=int(node.internalCount)/10, color="RoyalBlue", style="sphere")
T = TextFace("10")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
faces.add_face_to_node(T, node, 1)
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=0,
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 __layout__(self, node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
nstyle = NodeStyle()
nstyle["size"] = 0
node.set_style(nstyle)
if "internalCount" in node.features:
print node.name
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=int(node.internalCount) / 10,
color="RoyalBlue",
style="sphere")
T = TextFace("10")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
faces.add_face_to_node(T, node, 1)
def layout(node):
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=14, fgcolor=node.tip_color)
faces.add_face_to_node(N, node, 0)
def layout(node, feature):
if node.up is not None or feature == "id":
attr = AttrFace(feature, fsize=5, fgcolor="green")
faces.add_face_to_node(attr, node, 0, position="branch-top")
def mylayout(node, number_nodes=True, label_support_with_numbers=False):
#width is set to 2 to increase visibility in large trees when exporting
node.img_style["hz_line_width"]=4
node.img_style["vt_line_width"]=4
#counter2 = 0
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
node.img_style["size"] = 0
color = "#000000"
faces.add_face_to_node( faces.TextFace(node.name, ftype="Arial", fsize=20, fstyle = "italic", fgcolor=color), node, 0 )
#try adding the family to the tip as well
#if node.name in ranks:
#family = ranks[node.name]
#faces.add_face_to_node( faces.TextFace(family, ftype="Arial", fsize=12, fgcolor="red"), node, 0 )
if node.up is None:
node.img_style["size"]=0
node.dist = 0.35 # you may need to change this value to fit the aspect of your tree
node.img_style["hz_line_color"] = "#ffffff"
if UNROOTED:
node.img_style["vt_line_type"] = 0.001
#if node.name in face_dict:
# print "{} in face_dict ".format(node.name)
# faces.add_face_to_node(face_dict[node.name], node, column = 1, position = "branch-right") #WOuld relly like the image to appear on outside of tre
#print "found {} matches".format(counter2)
#node.img_style["size"] = 16
#node.img_style["shape"] = "sphere"
#node.img_style["fgcolor"] = "#AA0000"
# Sets the style of leaf nodes
#node.img_style["size"] = 12
#node.img_style["shape"] = "circle"
#If node is an internal node
else:
#support_face = CircleFace(radius=100, color="Thistle", style="circle")
#support_face.opacity = 0.3
#faces.add_face_to_node(support_face, node, 0, position="float")
###make bubble proportional to boostrap support
# Creates a sphere face whose size is proportional to node's
# feature "weight"
#C = CircleFace(radius=node.support, color="Black", style="sphere")
# Let's make the sphere transparent
#C.opacity = 1.0
# And place as a float face over the tree
#faces.add_face_to_node(C, node, 0, position="float")
#print "current node id :" + str(node.nodeid)
#print "is node in BG_COLORS? " + str(node.nodeid) in BG_COLORS
#if node.nodeid in BG_COLORS:
#print "this node is in colors" + node.nodeid
#node.img_style["bgcolor"] = BG_COLORS[str(node.nodeid)]
#print BG_COLORS[node.nodeid]
# Sets the style of internal nodes
node.img_style["size"] = 0
#node.img_style["shape"] = "circle"
#node.img_style["fgcolor"] = "#000000"
num = node.nodenumber
if number_nodes == True:
faces.add_face_to_node(faces.TextFace(num, ftype="Arial", fsize=12, fgcolor="purple"), node, 0, position = "branch-right")
# is the internal node an order?
if node.order:
faces.add_face_to_node(faces.TextFace(node.order, ftype="Arial", fsize=25, fgcolor="#black"), node, 0)
if label_support_with_numbers:
faces.add_face_to_node(faces.TextFace(node.support, ftype="Arial", fsize=10, fgcolor="black"), node, 0, position = "branch-top")
if node.bootstrap:
faces.add_face_to_node(faces.TextFace(node.bootstrap, ftype="Arial", fsize=10, fgcolor="grey"), node, 0, position = "branch-bottom")
makeSupportSymbols(node, node.bootstrap)
def my_layout(node):
# Add name label to all nodes
faces.add_face_to_node(AttrFace("name"),
node,
column=0,
position="branch-right")
def layout(node):
node.img_style["size"] = 5
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
if node.is_leaf():
f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
faces.add_face_to_node(f, node, 0, position="aligned")
f = faces.AttrFace("name", fsize=15)
faces.add_face_to_node(f, node, 0, position="branch-right")
else:
f = faces.TextFace("uno", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-top")
f = faces.TextFace("otromassssssssssss", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-bottom")
f = faces.CircleFace(20, "red")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float")
f = faces.CircleFace(23, "blue")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float-behind")