def barchart_layout(node, name='name',
width=20, height=40,
colors=None, min_value=0, max_value=1,
fsize=14, fgcolor="black"):
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=['#0000FF'], min_value=min_value,
max_value=max_value)
# Let's make the sphere transparent
C.opacity = 0.5
# Rotate the faces by 270*
C.rotation = 270
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
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)
def custom_layout(self,node):
if node.is_leaf():
aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=12)
aligned_name_face.margin_top = 5
aligned_name_face.margin_right = 5
aligned_name_face.margin_left = 5
aligned_name_face.margin_bottom = 5
aligned_name_face.hz_align = 0 #0 = left, 1 = center, 2 = right
add_face_to_node(aligned_name_face, node, column=2, position='aligned')
#name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
#name_face.margin_top = 3
#name_face.margin_right = 3
#name_face.margin_left = 3
#name_face.margin_bottom = 3
#add_face_to_node(name_face, node, column=2, position='branch-right')
node.img_style['size'] = 0
#---------------------------------------------
#displaying extra categorical and numeric data
if (node.name in self._tip2info):
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_data = self._tip2info[node.name][headerIndex]
if isinstance( extra_data, ( int, float ) ):
extra_face = BarChartFace([extra_data], width=100,height=25,colors=[self._tip2color[node.name][headerIndex]],labels=[dataheader],min_value=0.0,max_value=self._tip_max)
else:
extra_face = TextFace(extra_data, fsize=11, fgcolor='black')
extra_face.background.color = self._tip2color[node.name][headerIndex]
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
#add_face_to_node(extra_face, node, column=column_no, aligned = True, position='branch-right')
column_no += 1
else:
#print "No data available"
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_face = TextFace("No data available", fsize=10, fgcolor='black')
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
column_no += 1
image_col_no = column_no
#----------------------------------------------
if (node.name in self._img_chk_list):
if self._img_data_dic[node.name] is not None:
img_face = ImgFace(self._img_data_dic[node.name], is_url=True)
#img_face = ImgFace(self._tip2info[node.name][0], is_url=True)
#img_path = os.path.join("file:///home/tayeen/TayeenFolders/TreeViewer/WebTreeApp/newplugin_test/data/", "328653.jpg")
#img_face = ImgFace(img_path, is_url=True)
img_face.margin_top = 10
img_face.margin_right = 10
img_face.margin_left = 10
img_face.margin_bottom = 10
#add_face_to_node(img_face, node, column=3, position='branch-right')
#add_face_to_node(img_face, node, column=3, aligned= True, position='branch-right')
else:
img_path = os.path.join("file://"+image_path, "ina.jpg")
img_face = ImgFace(img_path, is_url=True)
#add_face_to_node(img_face, node, column=5, position='branch-right')
add_face_to_node(img_face, node, column=image_col_no, position='aligned')
else: #node is not a leaf
node.img_style['size'] = 4
node.img_style['shape'] = 'square'
if node.name and self._custom_options["draw_internal"]:
name_face = TextFace(node.name, fgcolor='grey', fsize=10)
name_face.margin_top = 4
name_face.margin_right = 4
name_face.margin_left = 4
name_face.margin_bottom = 4
add_face_to_node(name_face, node, column=0, position='branch-top')
if node.name in self._node2label:
label_face = TextFace(self._node2label[node.name], fgcolor='DarkGreen', fsize=10)
label_face.margin_top = 4
label_face.margin_right = 4
label_face.margin_left = 4
label_face.margin_bottom = 4
add_face_to_node(label_face, node, column=0, position="branch-top")
if node.support and self._custom_options["draw_support"]:
support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
support_face.margin_top = 4
support_face.margin_right = 4
support_face.margin_left = 4
support_face.margin_bottom = 4
add_face_to_node(support_face, node, column=0, position='branch-bottom')
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"]= False
collapsed_face = faces.TextFace(" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
# Parse node features features and conver them into styles. This must be done like this, since current ete version
#does not allow modifying style outside the layout function.
if hasattr(node, "bsize"):
node.img_style["size"]= int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"]= node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"]= node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"]= node.fgcolor
#parse all nodes features
if hasattr(node, "bh_bgcolor"):
node.img_style["bgcolor"]= node.bh_bgcolor
if hasattr(node, "bh_size"):
node.img_style["size"]= node.bh_size
if hasattr(node, "lh_color"):
node.img_style['hz_line_color'] = node.lh_color
node.img_style["vt_line_color"] = node.lh_color
if hasattr(node, "lh_width"):
node.img_style['hz_line_width'] = node.lh_width
node.img_style['vt_line_width'] = node.lh_width
if hasattr(node, "lh_width") and hasattr(node, "lh_color"):
for n in node.iter_descendants():
n.img_style['hz_line_color'] = node.lh_color
n.img_style["vt_line_color"] = node.lh_color
n.img_style['hz_line_width'] = node.lh_width
n.img_style['vt_line_width'] = node.lh_width