def _layout(node):
if self.hog is None:
_label = [str(node.nbr_genes),str(node.retained),str(node.dupl),str(node.gain),str(node.lost)]
else:
_label = [str(node.nbr_genes), str(node.retained), str(node.dupl), str(node.lost)]
def _add_face(name_feature, value_feature, cnum=1, pos="branch-right"):
node.add_face(TextFace("{}: {}".format(name_feature, value_feature)), column=cnum, position=pos)
def _add_faces(cNbr=1, posNbr="branch-right", cAttr=2, posAtt="branch-right"):
_add_face("#genes", node.nbr_genes, cnum=cNbr, pos=posNbr)
if node.retained is not None:
_add_face("#Retained", node.retained, cnum=cAttr, pos=posAtt)
if node.dupl is not None:
_add_face("#Duplicated", node.dupl, cnum=cAttr, pos=posAtt)
if node.gain is not None:
_add_face("#Novel", node.gain, cnum=cAttr, pos=posAtt)
if node.lost is not None:
_add_face("#Lost", node.lost, cnum=cAttr, pos=posAtt)
if node.is_leaf():
if display_internal_histogram:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes, node.retained, node.dupl, node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-right")
else:
_add_faces()
else:
if display_internal_histogram:
if node.is_root():
node.add_face(BarChartFace([node.nbr_genes], deviations=None, width=10, height=25, colors=["#41c1c2"], labels=[str(node.nbr_genes)], min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0, position = "branch-bottom")
else:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes,node.retained,node.dupl,node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-top")
else:
_add_faces(cNbr=0, posNbr="branch-top", cAttr=0, posAtt="branch-bottom")
def barchart_layout(node, name='name',
width=20, height=40,
colors=None, min_value=0, max_value=1,
fsize=14, fgcolor="black",
alpha=0.5,
rotation=270):
"""
Specifies the layout for the ete.TreeStyle object.
Parameters
----------
node: ete.Tree
Input node for specifying which attributes.
name: str, optional
Attribute to look up the name of the node.
width: int, optional
Width of the barchart.
height: int, optional
Height of the barchart.
colors: list of str, optional
List of HTML colors to color the barchart values.
min_value: int, optional
Minimum value to set the scale of the chart.
max_value: int, optional
Maximum value to set the scale of the chart.
fsize: int, optional
Font size on the leafs.
fgcolor: str, optional
Font color of the leafs.
alpha: float, optional
Transparency of the barchart.
rotation: int, optional
Orientation of the barchart.
"""
if colors is None:
colors = ['#0000FF']
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=fsize, fgcolor=fgcolor)
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"
if (isinstance(node.weight, int) or isinstance(node.weight, float)):
weight = [node.weight]
else:
weight = node.weight
C = BarChartFace(values=weight, width=width, height=height,
colors=colors, min_value=min_value,
max_value=max_value)
# Let's make the sphere transparent
C.opacity = alpha
# Rotate the faces by 270*
C.rotation = rotation
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def export(self, output, layout_function=None, display_internal_histogram=True):
"""
Method to export the tree profile object as figure (available format .SVG, .PDF, .PNG).
-- Some magic going there --
Args:
| output (:obj:`str`): output file name. The extension of output will set the format of the figure (SVG, .PDF, .PNG)
| layout_function (:obj:`function`, optional): custom layout_fn for ete3 TreeStyle.
| display_internal_histogram (:obj:`Boolean`, optional): Display internal node as histogram or raw text with numbers. Defaults to True.
"""
from ete3 import TreeStyle, TextFace, NodeStyle, BarChartFace
# maximum number of genes per node in this treeMap
max_genes = max([d for d in self.treemap.traverse()], key=lambda x:x.nbr_genes).nbr_genes
if self.hog is None:
_color_scheme = ["#41c1c2","#bdc3c7","#f39c12","#27ae60","#e74c3c"]
_label_legend = ["Genes","Retained","Duplicated","Novel","Lost"]
_values_legend = [max_genes,max_genes,max_genes,max_genes,max_genes]
w_legend = 50 # todo calculate base on len(_values)
else:
_color_scheme = ["#41c1c2", "#bdc3c7", "#f39c12", "#e74c3c"]
_label_legend = ["Genes", "Retained", "Duplicated", "Lost"]
_values_legend = [max_genes, max_genes, max_genes, max_genes]
w_legend = 40 # todo calculate base on len(_values)
def _layout(node):
if self.hog is None:
_label = [str(node.nbr_genes),str(node.retained),str(node.dupl),str(node.gain),str(node.lost)]
else:
_label = [str(node.nbr_genes), str(node.retained), str(node.dupl), str(node.lost)]
def _add_face(name_feature, value_feature, cnum=1, pos="branch-right"):
node.add_face(TextFace("{}: {}".format(name_feature, value_feature)), column=cnum, position=pos)
def _add_faces(cNbr=1, posNbr="branch-right", cAttr=2, posAtt="branch-right"):
_add_face("#genes", node.nbr_genes, cnum=cNbr, pos=posNbr)
if node.retained is not None:
_add_face("#Retained", node.retained, cnum=cAttr, pos=posAtt)
if node.dupl is not None:
_add_face("#Duplicated", node.dupl, cnum=cAttr, pos=posAtt)
if node.gain is not None:
_add_face("#Novel", node.gain, cnum=cAttr, pos=posAtt)
if node.lost is not None:
_add_face("#Lost", node.lost, cnum=cAttr, pos=posAtt)
if node.is_leaf():
if display_internal_histogram:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes, node.retained, node.dupl, node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-right")
else:
_add_faces()
else:
if display_internal_histogram:
if node.is_root():
node.add_face(BarChartFace([node.nbr_genes], deviations=None, width=10, height=25, colors=["#41c1c2"], labels=[str(node.nbr_genes)], min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0, position = "branch-bottom")
else:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes,node.retained,node.dupl,node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-top")
else:
_add_faces(cNbr=0, posNbr="branch-top", cAttr=0, posAtt="branch-bottom")
ts = TreeStyle()
if layout_function is not None:
ts.layout_fn = layout_function
else:
ts.layout_fn = _layout
ts.legend.add_face(BarChartFace(_values_legend, deviations=None, width=w_legend, height=25, colors=_color_scheme, labels=_label_legend, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0)
ts.legend_position = 3
self.treemap.render(output,tree_style=ts)