def mktreeNode(self, tuples): t = Tree() nstyle = NodeStyle() nstyle["shape"] = "sphere" nstyle["size"] = 10 nstyle["fgcolor"] = "darkred" # Gray dashed branch lines nstyle["hz_line_type"] = 1 nstyle["hz_line_color"] = "#cccccc" t.set_style(nstyle) if len(tuples) == 1: t.name = '(' + tuples[0][0] + ',' + tuples[0][1] + ')' else: t.name = "" return t
if len(args) < 1: parser.error("incorrect number of arguments") outfile_name = args[0] path_to_draw_map_task = args[1] lineage_files = args[2:] def print_recursive( id, tree ): print id print tree[id] for child in tree[id]['children'].keys(): print_recursive( child, tree ) tree = {} tree_phylogeny = Tree() ts = TreeStyle() ts.show_leaf_name = False ts.branch_vertical_margin = 10 #ts.scale = .1 def getNodeStyle( dictionary ): aStyle = NodeStyle() for key in dictionary.keys(): aStyle[key] = dictionary[key] return aStyle ## node styles
for name in names: if is_arabidopsis(name): for n in tree.get_leaves_by_name(name): nstyle = NodeStyle() nstyle["bgcolor"] = 'red' n.set_style(nstyle) else: for n in tree.get_leaves_by_name(name): nstyle = NodeStyle() nstyle["bgcolor"] = colour n.set_style(nstyle) #t = PhyloTree("RAxML_result.ITPR_LIKE_CHANNEL", alignment="hits_align.phy", alg_format="iphylip") #t.show() t = Tree(args.trees[0]) #Get leaves #names = t.get_leaf_names() #algae = filterNames(names, re.compile('.*ALGA.*').match) #plants = filterNames(names, re.compile('.*PLANT.*').match) #colourNodes(t,algae,"green") #colourNodes(t,plants,"#4ED34E") circle = TreeStyle() circle.show_leaf_name = True #circle.scale = 3 circle.mode = "c"