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from __future__ import absolute_import
from __future__ import print_function
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from .. import numpy
from . import faces
def basic(node):
if node.is_leaf():
node.img_style["size"]=2
node.img_style["shape"] = "square"
faces.add_face_to_node(faces.AttrFace("name","Arial",10,"#4f8f0f",None), node, 0 )
def phylogeny(node):
leaf_color = "#000000"
node.img_style["shape"] = "square"
node.img_style["size"] = 2
if hasattr(node,"evoltype"):
if node.evoltype == 'D':
node.img_style["fgcolor"] = "#FF0000"
node.img_style["hz_line_color"] = "#FF0000"
node.img_style["vt_line_color"] = "#FF0000"
elif node.evoltype == 'S':
node.img_style["fgcolor"] = "#1d176e"
node.img_style["hz_line_color"] = "#1d176e"
node.img_style["vt_line_color"] = "#1d176e"
elif node.evoltype == 'L':
node.img_style["fgcolor"] = "#777777"
node.img_style["vt_line_color"] = "#777777"
node.img_style["hz_line_color"] = "#777777"
node.img_style["hz_line_type"] = 1
node.img_style["vt_line_type"] = 1
leaf_color = "#777777"
if node.is_leaf():
node.img_style["shape"] = "square"
node.img_style["size"] = 2
node.img_style["fgcolor"] = leaf_color
faces.add_face_to_node( faces.AttrFace("name","Arial",11,leaf_color,None), node, 0 )
if hasattr(node,"sequence"):
SequenceFace = faces.SequenceFace(node.sequence,"aa",13)
faces.add_face_to_node(SequenceFace, node, 1, aligned=True)
else:
node.img_style["size"] = 2
def heatmap(node):
square_size = 10
# Extras node info
node.collapsed = False
# Color and style
node.img_style["fgcolor"] = "#3333FF"
node.img_style["size"] = 0
ncols = node.arraytable.matrix.shape[1]
matrix_max = numpy.max(node.arraytable._matrix_max)
matrix_min = numpy.min(node.arraytable._matrix_min)
matrix_avg = matrix_min+((matrix_max-matrix_min)/2)
ProfileFace = faces.ProfileFace(\
matrix_max,\
matrix_min,\
matrix_avg,\
square_size*ncols,\
square_size,\
"heatmap")
ProfileFace.ymargin=0
if node.is_leaf():
# Set colors
faces.add_face_to_node(ProfileFace, node, 0, aligned=True)
def cluster_cbars(node):
# Extras node info
node.collapsed = False
# Color and style
node.img_style["fgcolor"] = "#3333FF"
node.img_style["size"] = 4
matrix_max = numpy.max(node.arraytable._matrix_max)
matrix_min = numpy.min(node.arraytable._matrix_min)
matrix_avg = matrix_min+((matrix_max-matrix_min)/2)
ProfileFace = faces.ProfileFace(\
matrix_max,\
matrix_min,\
matrix_avg,\
200,\
60,\
"cbars")
if node.is_leaf():
nameFace = faces.AttrFace("name",fsize=6 )
faces.add_face_to_node(nameFace, node, 1, aligned=True )
faces.add_face_to_node(ProfileFace, node, 0, aligned=True )
else:
# Set custom faces
faces.add_face_to_node(ProfileFace, node, 0, aligned=True )
def cluster_lines(node):
# Extras node info
node.collapsed = False
# Color and style
node.img_style["fgcolor"] = "#3333FF"
node.img_style["size"] = 4
matrix_max = numpy.max(node.arraytable._matrix_max)
matrix_min = numpy.min(node.arraytable._matrix_min)
matrix_avg = matrix_min+((matrix_max-matrix_min)/2)
ProfileFace = faces.ProfileFace(\
matrix_max,\
matrix_min,\
matrix_avg,\
200,\
50,\
"lines")
if node.is_leaf():
nameFace = faces.AttrFace("name",fsize=6 )
faces.add_face_to_node(nameFace, node, 1, aligned=True )
faces.add_face_to_node(ProfileFace, node, 0, aligned=True )
else:
# Set custom faces
faces.add_face_to_node(ProfileFace, node, 0, aligned=True )
def cluster_bars(node):
# Extras node info
node.collapsed = False
# Color and style
node.img_style["fgcolor"] = "#3333FF"
node.img_style["size"] = 4
if node.is_leaf():
matrix_max = numpy.max(node.arraytable._matrix_max)
matrix_min = numpy.min(node.arraytable._matrix_min)
matrix_avg = matrix_min+((matrix_max-matrix_min)/2)
ProfileFace = faces.ProfileFace(\
matrix_max,\
matrix_min,\
matrix_avg,\
200,\
40,\
"bars")
nameFace = faces.AttrFace("name",fsize=6 )
faces.add_face_to_node(nameFace, node, 1, aligned=True )
faces.add_face_to_node(ProfileFace, node, 0, aligned=True )
def large(node):
# Color and style
node.img_style["fgcolor"] = "#3333FF"
node.img_style["size"] = 0
def evol_layout(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
leaf_color = "#000000"
if not node.is_root() and 'w' in node.features:
node.img_style["shape"] = 'circle'
if (node.w > 900):
node._w = 3
elif (node.w > 100):
node._w = 2.5
elif (node.w > 10) :
node._w = 2
elif (node.w > 1):
node._w = 1.5
else:
node._w = node.w
node.img_style["size"] = int ((float(node._w))*6+2)
if node._w == 3 :
node.img_style["fgcolor"] = "#c10000"
if node._w == 2.5 :
node.img_style["fgcolor"] = "#FF5A02"
if node._w == 2 :
node.img_style["fgcolor"] = "#FFA200"
if node._w == 1.5 :
node.img_style["fgcolor"] = "#E9BF00"
if node._w < 0.2 :
node.img_style["fgcolor"] = "#000000"
if hasattr(node,"extras"):
faces.add_face_to_node( faces.AttrFace("extras", "Arial", 7, \
"#000000", None), node, 2 )
#if node.is_leaf():
if hasattr (node, "sequence"):
seqface = faces.SequenceFace(node.sequence, interactive=True,
codon=node.nt_sequence)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def evol_clean_layout(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
leaf_color = "#000000"
node.img_style["size"] = 2
if node.is_leaf():
#if hasattr (node,"highlight"):
# faces.add_face_to_node(faces.AttrFace("name", "Arial", 9, \
# node.highlight,
# None), \
# node, 0 )
#else:
# leaface = faces.AttrFace("name", "Arial", 9, leaf_color, None)
# leaface.margin_right = 10
# faces.add_face_to_node (leaface, node, 0)
if hasattr (node, "sequence"):
seqface = faces.SequenceFace(node.sequence, interactive=True,
codon=node.nt_sequence)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if hasattr(node, 'dN'):
faces.add_face_to_node (faces.TextFace('%.4f'%(node.w), fsize=6,
fgcolor="#7D2D2D"),
node, 0, position="branch-top")
faces.add_face_to_node (faces.TextFace('%.2f/%.2f'% (100*node.dN,
100*node.dS),
fsize=6, fgcolor="#787878"),
node, 0, position="branch-bottom")
if hasattr(node,"extras"):
faces.add_face_to_node( faces.AttrFace("extras", "Arial", 7, \
"#000000", None), node, 2 )
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