def draw_tree(tree, conf, outfile): try: from ete2 import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace, SequenceFace, random_color, SeqMotifFace) except ImportError as e: print e return def ly_basic(node): if node.is_leaf(): node.img_style['size'] = 0 else: node.img_style['size'] = 0 node.img_style['shape'] = 'square' if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"): if node.tree_seqtype == "nt": node.img_style["bgcolor"] = "#CFE6CA" ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica') add_face_to_node(ntF, node, 10, position="branch-bottom") if len(NPR_TREES) > 1 and hasattr(node, "tree_type"): node.img_style['size'] = 4 node.img_style['fgcolor'] = "steelblue" node.img_style['hz_line_width'] = 1 node.img_style['vt_line_width'] = 1 def ly_leaf_names(node): if node.is_leaf(): spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica') add_face_to_node(spF, node, column=0, position='branch-right') if hasattr(node, 'genename'): geneF = TextFace(" (%s)" % node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica') add_face_to_node(geneF, node, column=1, position='branch-right') def ly_supports(node): if not node.is_leaf() and node.up: supFace = TextFace("%0.2g" % (node.support), fsize=7, fgcolor='indianred') add_face_to_node(supFace, node, column=0, position='branch-top') def ly_tax_labels(node): if node.is_leaf(): c = LABEL_START_COL largest = 0 for tname in TRACKED_CLADES: if hasattr(node, "named_lineage") and tname in node.named_lineage: linF = TextFace(tname, fsize=10, fgcolor='white') linF.margin_left = 3 linF.margin_right = 2 linF.background.color = lin2color[tname] add_face_to_node(linF, node, c, position='aligned') c += 1 for n in xrange(c, len(TRACKED_CLADES)): add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned') c += 1 def ly_full_alg(node): pass def ly_block_alg(node): if node.is_leaf(): if 'sequence' in node.features: seqFace = SeqMotifFace(node.sequence, []) # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"], motifs = [] last_lt = None for c, lt in enumerate(node.sequence): if lt != '-': if last_lt is None: last_lt = c if c + 1 == len(node.sequence): start, end = last_lt, c motifs.append([ start, end, "()", 0, 12, "slategrey", "slategrey", None ]) last_lt = None elif lt == '-': if last_lt is not None: start, end = last_lt, c - 1 motifs.append([ start, end, "()", 0, 12, "grey", "slategrey", None ]) last_lt = None seqFace = SeqMotifFace(node.sequence, motifs, intermotif_format="line", seqtail_format="line", scale_factor=ALG_SCALE) add_face_to_node(seqFace, node, ALG_START_COL, aligned=True) TRACKED_CLADES = [ "Eukaryota", "Viridiplantae", "Fungi", "Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta", "Amoebozoa", "Crypthophyta", "Bacteria", "Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria", "Gammaproteobacteria", ] # ["Opisthokonta", "Apicomplexa"] colors = random_color(num=len(TRACKED_CLADES), s=0.45) lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)]) NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444') LABEL_START_COL = 10 ALG_START_COL = 40 ts = TreeStyle() ts.draw_aligned_faces_as_table = False ts.draw_guiding_lines = False ts.show_leaf_name = False ts.show_branch_support = False ts.scale = 160 ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels] MIXED_RES = set() MAX_SEQ_LEN = 0 NPR_TREES = [] for n in tree.traverse(): if hasattr(n, "tree_seqtype"): MIXED_RES.add(n.tree_seqtype) if hasattr(n, "tree_type"): NPR_TREES.append(n.tree_type) seq = getattr(n, "sequence", "") MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN) if MAX_SEQ_LEN: ALG_SCALE = min(1, 1000. / MAX_SEQ_LEN) ts.layout_fn.append(ly_block_alg) if len(NPR_TREES) > 1: rF = RectFace(4, 4, "steelblue", "steelblue") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" NPR node"), 1) ts.legend_position = 3 if len(MIXED_RES) > 1: rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1) ts.legend_position = 3 try: tree.set_species_naming_function(spname) annotate_tree_with_ncbi(tree) a = tree.search_nodes(species='Dictyostelium discoideum')[0] b = tree.search_nodes(species='Chondrus crispus')[0] #out = tree.get_common_ancestor([a, b]) #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up tree.set_outgroup(out) tree.swap_children() except Exception: pass tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150) tree.render(outfile + '.svg', tree_style=ts, w=170, units='mm', dpi=150) tree.render(outfile + '.pdf', tree_style=ts, w=170, units='mm', dpi=150)
def draw_tree(tree, conf, outfile): try: from ete2 import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace, SequenceFace, random_color, SeqMotifFace) except ImportError as e: print e return def ly_basic(node): if node.is_leaf(): node.img_style['size'] = 0 else: node.img_style['size'] = 0 node.img_style['shape'] = 'square' if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"): if node.tree_seqtype == "nt": node.img_style["bgcolor"] = "#CFE6CA" ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica') add_face_to_node(ntF, node, 10, position="branch-bottom") if len(NPR_TREES) > 1 and hasattr(node, "tree_type"): node.img_style['size'] = 4 node.img_style['fgcolor'] = "steelblue" node.img_style['hz_line_width'] = 1 node.img_style['vt_line_width'] = 1 def ly_leaf_names(node): if node.is_leaf(): spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica') add_face_to_node(spF, node, column=0, position='branch-right') if hasattr(node, 'genename'): geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica') add_face_to_node(geneF, node, column=1, position='branch-right') def ly_supports(node): if not node.is_leaf() and node.up: supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred') add_face_to_node(supFace, node, column=0, position='branch-top') def ly_tax_labels(node): if node.is_leaf(): c = LABEL_START_COL largest = 0 for tname in TRACKED_CLADES: if hasattr(node, "named_lineage") and tname in node.named_lineage: linF = TextFace(tname, fsize=10, fgcolor='white') linF.margin_left = 3 linF.margin_right = 2 linF.background.color = lin2color[tname] add_face_to_node(linF, node, c, position='aligned') c += 1 for n in xrange(c, len(TRACKED_CLADES)): add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned') c+=1 def ly_full_alg(node): pass def ly_block_alg(node): if node.is_leaf(): if 'sequence' in node.features: seqFace = SeqMotifFace(node.sequence, []) # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"], motifs = [] last_lt = None for c, lt in enumerate(node.sequence): if lt != '-': if last_lt is None: last_lt = c if c+1 == len(node.sequence): start, end = last_lt, c motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None]) last_lt = None elif lt == '-': if last_lt is not None: start, end = last_lt, c-1 motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None]) last_lt = None seqFace = SeqMotifFace(node.sequence, motifs, intermotif_format="line", seqtail_format="line", scale_factor=ALG_SCALE) add_face_to_node(seqFace, node, ALG_START_COL, aligned=True) TRACKED_CLADES = ["Eukaryota", "Viridiplantae", "Fungi", "Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta", "Amoebozoa", "Crypthophyta", "Bacteria", "Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria", "Gammaproteobacteria",] # ["Opisthokonta", "Apicomplexa"] colors = random_color(num=len(TRACKED_CLADES), s=0.45) lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)]) NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444') LABEL_START_COL = 10 ALG_START_COL = 40 ts = TreeStyle() ts.draw_aligned_faces_as_table = False ts.draw_guiding_lines = False ts.show_leaf_name = False ts.show_branch_support = False ts.scale = 160 ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels] MIXED_RES = set() MAX_SEQ_LEN = 0 NPR_TREES = [] for n in tree.traverse(): if hasattr(n, "tree_seqtype"): MIXED_RES.add(n.tree_seqtype) if hasattr(n, "tree_type"): NPR_TREES.append(n.tree_type) seq = getattr(n, "sequence", "") MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN) if MAX_SEQ_LEN: ALG_SCALE = min(1, 1000./MAX_SEQ_LEN) ts.layout_fn.append(ly_block_alg) if len(NPR_TREES) > 1: rF = RectFace(4, 4, "steelblue", "steelblue") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" NPR node"), 1) ts.legend_position = 3 if len(MIXED_RES) > 1: rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1) ts.legend_position = 3 try: tree.set_species_naming_function(spname) annotate_tree_with_ncbi(tree) a = tree.search_nodes(species='Dictyostelium discoideum')[0] b = tree.search_nodes(species='Chondrus crispus')[0] #out = tree.get_common_ancestor([a, b]) #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up tree.set_outgroup(out) tree.swap_children() except Exception: pass tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150) tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150) tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
from ete2 import EvolTree from ete2 import faces tree = EvolTree("data/S_example/measuring_S_tree.nw") tree.link_to_alignment("data/S_example/alignment_S_measuring_evol.fasta") print tree print "\n Running free-ratio model with calculation of ancestral sequences..." tree.run_model("fb_anc") # tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc') I = TreeStyle() I.force_topology = False I.draw_aligned_faces_as_table = True I.draw_guiding_lines = True I.guiding_lines_type = 2 I.guiding_lines_color = "#CCCCCC" for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id): if n.is_leaf(): continue anc_face = faces.SequenceFace(n.sequence, "aa", fsize=10, bg_colors={}) I.aligned_foot.add_face(anc_face, 1) I.aligned_foot.add_face(faces.TextFace("node_id: #%d " % (n.node_id), fsize=8), 0) print "display result of bs_anc model, with ancestral amino acid sequences." tree.show(tree_style=I) print "\nThe End."
column_color.extend(colors) column_header.append("") column_color.append("black") spaciators.add(len(column_header) - 1) header2column = dict([(name, i) for i, name in enumerate(column_header)]) ts = TreeStyle() ts.mode = 'r' ts.draw_guiding_lines = False ts.show_leaf_name = False ts.force_topology = False ts.layout_fn = layout ts.tree_width = 800 ts.draw_aligned_faces_as_table = True for i, name in enumerate(column_header): if name: headerF = TextFace(str(name), fgcolor=column_color[i], fsize=40) headerF.rotation = -85 else: headerF = RectFace(300, 5, "white", "white") ts.aligned_header.add_face(headerF, i) #tree_files = sys.argv[1:] for treefile in args.tree_files: output = treefile + '.png' print 'rendering', output try: t = Tree(open(treefile).read().replace('|', ','))