def botstrap_symbols(node):
node_style = color_subtypes(node)
if hasattr(node, "suport_symbol"):
add_face_to_node(
face=TextFace(node.suport_symbol),
node=node,
column=0,
)
node.set_style(node_style)
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
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 = TextFace("Silh=%0.2f" % node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"] = "#056600"
# Otherwise, use red bubbles
else:
validationFace = 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
add_face_to_node(validationFace, node, 0)
if len(node) > 100:
add_face_to_node(cbarsFace, node, 1)
def mylayout(node):
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = ProfileFace(matrix_max,matrix_min,matrix_avg,200,70,"cbars")
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=0
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 = TextFace("Silh=%0.2f" %node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"]="#056600"
# Otherwise, use red bubbles
else:
validationFace = 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
add_face_to_node(validationFace, node, 0)
if len(node)>100:
add_face_to_node(cbarsFace, node, 1)
def sel_mylayout(node):
node.set_style(my_node_style)
if node.is_leaf():
# add names in larger font + italics
species_name = AttrFace("name", fsize=12, fstyle="italic")
add_face_to_node(species_name,
node,
column=0,
position="branch-right")
# add absence/presence matrix
for i, value in enumerate(getattr(node, "profile", [])):
if value > 0:
color = "#FF0000"
else:
color = "#EEEEEE"
my_face = CircleFace(8, color, style="circle")
my_face.margin_right = 3
my_face.margin_bottom = 3
add_face_to_node(my_face, node, position="aligned", column=i)
def diamond_layout(node):
# Run the layout passed in first before
# filling in the heatmap
layout(node)
N = AttrFace("name", fsize=label_size, fgcolor=labelcolor)
# background colors
c, found = _get_node_color(bgcolors, node, "")
if found:
nst = NodeStyle()
nst["bgcolor"] = c
node.set_style(nst)
if node.name in collapsed_nodes:
# scaling factor for approximating subtree depth
depth = node.get_farthest_leaf(topology_only=True)
w = depth[1] * depth_scaling
# scaling factor for approximating for subtree width
h = len(node) * breadth_scaling
c, _ = _get_node_color(cladecolors, node, "#0000FF")
C = CollapsedDiamondFace(width=w, height=h, color=c)
node.img_style['draw_descendants'] = False
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
faces.add_face_to_node(N, node, 1, position="float")
else:
faces.add_face_to_node(N, node, 0)
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=2