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 . # # # 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 )