def render_annotate(newick_path, output_path): """Render the annotated tree, showing internal node names. The output_path should end in .PNG, .PDF or .SVG: this will determine the format. To aid in testing, if output_path is None, the tree is shown rather than rendered. """ tree = Tree(newick_path, format=1) ts = TreeStyle() ts.show_leaf_name = True ts.branch_vertical_margin = 15 ns = NodeStyle() ns["size"] = 1 edge = 0 for node in tree.traverse(): node.name = node.name.replace("'", "") node.name = node.name.replace("+", ",") if not node.is_leaf() and node.name != 'NoName': f = TextFace(node.name) f.margin_top = 5 f.margin_bottom = 5 f.margin_right = 10 f.margin_left = 10 edge += 1 node.add_face(f, column=0, position="branch-top") if output_path is None: tree.show(tree_style=ts) else: tree.render(output_path)
def draw_tree(tree, file): root = tree.get_midpoint_outgroup() try: tree.set_outgroup(root) except: pass root = tree.get_tree_root() root.dist = 0 add_sig(tree) ts = TreeStyle() ts.branch_vertical_margin = 1 #ts.scale = 1500 ts.show_leaf_name = False #ts.show_branch_support = True leg_file = path.join(path.expanduser('~'), 'Perl', 'Modules', 'TreeLegend.png') leg_face= ImgFace(img_file=leg_file) leg_face.margin_left, leg_face.margin_top = 5, 5 ts.legend.add_face(leg_face, column=1) ts.legend_position=1 title_face = TextFace(text=file.split('.')[0]) title_face.margin_left, title_face.margin_top = 10, 5 ts.title.add_face(title_face, column=1) (ts.margin_left, ts.margin_right) = (5,5) tree.render(file, tree_style=ts, w=6000, units='mm')
def make_tree(treefile, image_file, clone_info): colour_list = ['MidnightBlue','RoyalBlue', 'LightSkyBlue', 'Aquamarine', 'SpringGreen', 'GreenYellow',\ 'Gold','DarkOrange'] weeks = ['16', '30', '38', '48', '59', '119', '176', '206'] weeks = ['6', '14', '53', '92','144'] t = Tree(treefile,format = 1) ts = TreeStyle() for i in range(5): ts.legend.add_face(CircleFace(20, colour_list[i]), column=0) ts.legend.add_face(TextFace('week' + weeks[i]), column=1) ts.legend_position = 2 ts.show_leaf_name = True ts.branch_vertical_margin = 15 ts.rotation = 90 ns = NodeStyle() ns["size"] = 1 ns.hz_line_width = 10 ns.vt_line_width = 10 edge = 0 for node in t.traverse(): node.name = node.name.replace("'", "") node.name = node.name.replace(".", ",") name = node.name.split(' ')[0] print name if name in clone_info.keys(): style_node(node, colour_list[int(clone_info[name][0])-1], int(int(clone_info[name][1])/10)+5) if not node.is_leaf() and node.name != 'NoName': f = TextFace(node.name) f.margin_top = 2.5 f.margin_bottom = 2.5 f.margin_right = 2.5 f.margin_left = 2.5 node.add_face(f, column=0, position="branch-top") t.render(image_file, tree_style = ts)
def render_annotate(newick_path, output_path): """Render the annotated tree, showing internal node names. The output_path should end in .PNG, .PDF or .SVG: this will determine the format. To aid in testing, if output_path is None, the tree is shown rather than rendered. """ tree = Tree(newick_path, format=1) ts = TreeStyle() ts.show_leaf_name = True ts.branch_vertical_margin = 15 ns = NodeStyle() ns["size"] = 1 edge = 0 for node in tree.traverse(): node.name = node.name.replace("'", "") node.name = node.name.replace("+", ",") if not node.is_leaf() and node.name != "NoName": f = TextFace(node.name) f.margin_top = 5 f.margin_bottom = 5 f.margin_right = 10 f.margin_left = 10 edge += 1 node.add_face(f, column=0, position="branch-top") if output_path is None: tree.show(tree_style=ts) else: tree.render(output_path)
def add_faces(cur, field, leaf, label_info, colours, bg_colour, outfile): y = 0 for x in range(len(label_info)): if x == 0: label_info[x] += ':' elif x < len(label_info) - 1: label_info[x] += ',' if '.svg' in outfile: padding = 1 + len(label_info[x]) /5 #this isn't label_info[x] += ' ' * padding label = TextFace(label_info[x]) if '.svg' in outfile: label.margin_left = 20 else: label.margin_left = 5 label.fgcolor = colours[x] label.background.color = bg_colour if x > 1 and x % 3 == 0: y += 3 leaf.add_face(label, column=x-y+1, position="branch-right")
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 layout(node): node.img_style["size"] = 0 node.img_style['hz_line_width'] = 2 node.img_style['vt_line_width'] = 2 if node.is_leaf(): # parse names fields = node.orig_name.split("__") name = fields[1].replace('_', ' ') code = "%s" %fields[0].strip() # Specie name nF = TextFace(name, fsize=12, fgcolor='#444', fstyle='italic') add_face_to_node(nF, node, column=0, position='aligned') # Species code cF = TextFace(code, fsize=12, fgcolor='grey') cF.margin_left = 4 cF.margin_right = 4 add_face_to_node(cF, node, column=1, position='branch-right') # Lead node styling node.img_style['hz_line_color'] = "green" node.img_style['vt_line_color'] = "green" else: # L90: green, L70: blue, L50: dark blue, L30: pink and L10: red. For the species # tree discordance test we collapse all branches below L90. B = float(node.B) if B >= 90: color = "green" elif B >= 70: color = "blue" elif B >= 50: color = "darkblue" elif B >= 30: color = "pink" elif B >= 10: color = "red" else: color = "yellow" node.img_style['hz_line_color'] = color node.img_style['vt_line_color'] = color
def main(): args = parse_args() if args.data: print "\nReading tree from " + args.tree + " and data matrix from " + args.data tree = ClusterTree(args.tree, text_array=args.data) else: print "\nReading tree from " + args.tree tree = Tree(args.tree) if args.midpoint: R = tree.get_midpoint_outgroup() tree.set_outgroup(R) print "- Applying midpoint rooting" elif args.outgroup: tree.set_outgroup(tree & args.outgroup) print "- Rooting using outgroup " + args.outgroup if not args.no_ladderize: tree.ladderize() print "- Ladderizing tree" table, column_list, column_values = readtable(args, tree.get_leaf_names()) labels = [] if args.labels: print "\nThese labels will be printed next to each strain:" for label in args.labels: if label in column_list: labels.append(label) print " " + label else: print "WARNING: specified label " + label + " was not found in the columns of the info file provided, " + args.info # set node styles # start by setting all to no shapes, black labels for n in tree.traverse(): nstyle = NodeStyle() nstyle["fgcolor"] = "black" nstyle["size"] = 0 n.set_style(nstyle) # add colour tags next to nodes if args.colour_tags: colour_tags = [] print "\nThese columns will be used to generate colour tags:" for label in args.colour_tags: if label in column_list: colour_tags.append(label) print " " + label else: print "\tWARNING: specified label for colour tagging, " + label + ", was not found in the columns of the info file provided, " + args.info print(colour_tags) print("here") for i in range(0, len(colour_tags)): label = colour_tags[i] print(label) colour_dict = getColourPalette(column_values[label], args, label) print "- Adding colour tag for " + label for node in tree.get_leaves(): this_face = Face() this_face.margin_left = args.padding node.add_face(this_face, column=0, position="aligned") if node.name in table: this_label = table[node.name][label] this_colour = colour_dict[this_label] else: this_colour = "white" this_face = Face() this_face.background.color = this_colour this_face.margin_right = args.margin_right this_face.margin_left = args.margin_left this_face.margin_top = args.margin_top this_face.margin_bottom = args.margin_bottom this_face.border.width = args.border_width this_face.border.color = "white" node.add_face(this_face, column=i + 1, position="aligned") print else: colour_tags = [] # add labels as columns for i in range(0, len(labels)): label = labels[i] print "- Adding label " + label if label == args.colour_nodes_by: print " also colouring nodes by these values" print(column_values) print(args) colour_dict = getColourPalette(column_values[label], args, label) for node in tree.get_leaves(): if node.name in table: this_label = table[node.name][label] this_colour = colour_dict[this_label] else: this_label = "" this_colour = "black" this_face = TextFace(text=this_label, fsize=args.font_size) if args.tags: this_face.background.color = this_colour elif label == args.colour_nodes_by: this_face.fgcolor = this_colour this_face.margin_right = args.padding if i == 0: this_face.margin_left = args.padding node.add_face(this_face, column=i + len(colour_tags) + 1, position="aligned") # set leaves to coloured circles node.img_style["size"] = args.node_size if label == args.colour_nodes_by: node.img_style["fgcolor"] = this_colour if args.colour_branches_by or args.colour_backgrounds_by or args.branch_support_colour: if args.colour_branches_by: print "- Colouring branches by label " + args.colour_branches_by colour_dict_br = getColourPalette( column_values[args.colour_branches_by], args, args.colour_branches_by) if args.colour_backgrounds_by: print "- Colouring node backgrounds by label " + args.colour_backgrounds_by colour_dict_bg = getColourPalette( column_values[args.colour_backgrounds_by], args, args.colour_backgrounds_by) if args.branch_support_colour: print "- Colouring branches by support values" # colours extracted from R using rgb( colorRamp(c("white","red", "black"))(seq(0, 1, length = 100)), max = 255) # support_colours = {0.0:"#FFFFFF",0.01:"#FFFFFF", 0.02:"#FFF9F9", 0.03:"#FFF4F4", 0.04:"#FFEFEF", 0.05:"#FFEAEA", 0.06:"#FFE5E5", 0.07:"#FFE0E0", 0.08:"#FFDADA", 0.09:"#FFD5D5", 0.1:"#FFD0D0", 0.11:"#FFCBCB", 0.12:"#FFC6C6", 0.13:"#FFC1C1", 0.14:"#FFBCBC", 0.15:"#FFB6B6", 0.16:"#FFB1B1", 0.17:"#FFACAC", 0.18:"#FFA7A7", 0.19:"#FFA2A2", 0.2:"#FF9D9D", 0.21:"#FF9797", 0.22:"#FF9292", 0.23:"#FF8D8D", 0.24:"#FF8888", 0.25:"#FF8383", 0.26:"#FF7E7E", 0.27:"#FF7979", 0.28:"#FF7373", 0.29:"#FF6E6E", 0.3:"#FF6969", 0.31:"#FF6464", 0.32:"#FF5F5F", 0.33:"#FF5A5A", 0.34:"#FF5454", 0.35:"#FF4F4F", 0.36:"#FF4A4A", 0.37:"#FF4545", 0.38:"#FF4040", 0.39:"#FF3B3B", 0.4:"#FF3636", 0.41:"#FF3030", 0.42:"#FF2B2B", 0.43:"#FF2626", 0.44:"#FF2121", 0.45:"#FF1C1C", 0.46:"#FF1717", 0.47:"#FF1212", 0.48:"#FF0C0C", 0.49:"#FF0707", 0.5:"#FF0202", 0.51:"#FC0000", 0.52:"#F70000", 0.53:"#F20000", 0.54:"#EC0000", 0.55:"#E70000", 0.56:"#E20000", 0.57:"#DD0000", 0.58:"#D80000", 0.59:"#D30000", 0.6:"#CE0000", 0.61:"#C80000", 0.62:"#C30000", 0.63:"#BE0000", 0.64:"#B90000", 0.65:"#B40000", 0.66:"#AF0000", 0.67:"#A90000", 0.68:"#A40000", 0.69:"#9F0000", 0.7:"#9A0000", 0.71:"#950000", 0.72:"#900000", 0.73:"#8B0000", 0.74:"#850000", 0.75:"#800000", 0.76:"#7B0000", 0.77:"#760000", 0.78:"#710000", 0.79:"#6C0000", 0.8:"#670000", 0.81:"#610000", 0.82:"#5C0000", 0.83:"#570000", 0.84:"#520000", 0.85:"#4D0000", 0.86:"#480000", 0.87:"#420000", 0.88:"#3D0000", 0.89:"#380000", 0.9:"#330000", 0.91:"#2E0000", 0.92:"#290000", 0.93:"#240000", 0.94:"#1E0000", 0.95:"#190000", 0.96:"#140000", 0.97:"#0F0000", 0.98:"#0A0000", 0.99:"#050000", 1:"#000000"} # rgb( colorRamp(c("red", "black"))(seq(0, 1, length = 100)), max = 255)) support_colours = {} if args.branch_support_cutoff: for i in range(0, args.branch_support_cutoff): support_colours[i] = "#FF0000" for i in range(args.branch_support_cutoff, 101): support_colours[i] = "#000000" else: if args.branch_support_percent: support_colours = { 0: "#FF0000", 1: "#FF0000", 2: "#FC0000", 3: "#F90000", 4: "#F70000", 5: "#F40000", 6: "#F20000", 7: "#EF0000", 8: "#EC0000", 9: "#EA0000", 10: "#E70000", 11: "#E50000", 12: "#E20000", 13: "#E00000", 14: "#DD0000", 15: "#DA0000", 16: "#D80000", 17: "#D50000", 18: "#D30000", 19: "#D00000", 20: "#CE0000", 21: "#CB0000", 22: "#C80000", 23: "#C60000", 24: "#C30000", 25: "#C10000", 26: "#BE0000", 27: "#BC0000", 28: "#B90000", 29: "#B60000", 30: "#B40000", 31: "#B10000", 32: "#AF0000", 33: "#AC0000", 34: "#AA0000", 35: "#A70000", 36: "#A40000", 37: "#A20000", 38: "#9F0000", 39: "#9D0000", 40: "#9A0000", 41: "#970000", 42: "#950000", 43: "#920000", 44: "#900000", 45: "#8D0000", 46: "#8B0000", 47: "#880000", 48: "#850000", 49: "#830000", 50: "#800000", 51: "#7E0000", 52: "#7B0000", 53: "#790000", 54: "#760000", 55: "#730000", 56: "#710000", 57: "#6E0000", 58: "#6C0000", 59: "#690000", 60: "#670000", 61: "#640000", 62: "#610000", 63: "#5F0000", 64: "#5C0000", 65: "#5A0000", 66: "#570000", 67: "#540000", 68: "#520000", 69: "#4F0000", 70: "#4D0000", 71: "#4A0000", 72: "#480000", 73: "#450000", 74: "#420000", 75: "#400000", 76: "#3D0000", 77: "#3B0000", 78: "#380000", 79: "#360000", 80: "#330000", 81: "#300000", 82: "#2E0000", 83: "#2B0000", 84: "#290000", 85: "#260000", 86: "#240000", 87: "#210000", 88: "#1E0000", 89: "#1C0000", 90: "#190000", 91: "#170000", 92: "#140000", 93: "#120000", 94: "#0F0000", 95: "#0C0000", 96: "#0A0000", 97: "#070000", 98: "#050000", 99: "#020000", 100: "#000000" } else: support_colours = { 0.0: "#FF0000", 0.01: "#FF0000", 0.02: "#FC0000", 0.03: "#F90000", 0.04: "#F70000", 0.05: "#F40000", 0.06: "#F20000", 0.07: "#EF0000", 0.08: "#EC0000", 0.09: "#EA0000", 0.1: "#E70000", 0.11: "#E50000", 0.12: "#E20000", 0.13: "#E00000", 0.14: "#DD0000", 0.15: "#DA0000", 0.16: "#D80000", 0.17: "#D50000", 0.18: "#D30000", 0.19: "#D00000", 0.2: "#CE0000", 0.21: "#CB0000", 0.22: "#C80000", 0.23: "#C60000", 0.24: "#C30000", 0.25: "#C10000", 0.26: "#BE0000", 0.27: "#BC0000", 0.28: "#B90000", 0.29: "#B60000", 0.3: "#B40000", 0.31: "#B10000", 0.32: "#AF0000", 0.33: "#AC0000", 0.34: "#AA0000", 0.35: "#A70000", 0.36: "#A40000", 0.37: "#A20000", 0.38: "#9F0000", 0.39: "#9D0000", 0.4: "#9A0000", 0.41: "#970000", 0.42: "#950000", 0.43: "#920000", 0.44: "#900000", 0.45: "#8D0000", 0.46: "#8B0000", 0.47: "#880000", 0.48: "#850000", 0.49: "#830000", 0.5: "#800000", 0.51: "#7E0000", 0.52: "#7B0000", 0.53: "#790000", 0.54: "#760000", 0.55: "#730000", 0.56: "#710000", 0.57: "#6E0000", 0.58: "#6C0000", 0.59: "#690000", 0.6: "#670000", 0.61: "#640000", 0.62: "#610000", 0.63: "#5F0000", 0.64: "#5C0000", 0.65: "#5A0000", 0.66: "#570000", 0.67: "#540000", 0.68: "#520000", 0.69: "#4F0000", 0.7: "#4D0000", 0.71: "#4A0000", 0.72: "#480000", 0.73: "#450000", 0.74: "#420000", 0.75: "#400000", 0.76: "#3D0000", 0.77: "#3B0000", 0.78: "#380000", 0.79: "#360000", 0.8: "#330000", 0.81: "#300000", 0.82: "#2E0000", 0.83: "#2B0000", 0.84: "#290000", 0.85: "#260000", 0.86: "#240000", 0.87: "#210000", 0.88: "#1E0000", 0.89: "#1C0000", 0.9: "#190000", 0.91: "#170000", 0.92: "#140000", 0.93: "#120000", 0.94: "#0F0000", 0.95: "#0C0000", 0.96: "#0A0000", 0.97: "#070000", 0.98: "#050000", 0.99: "#020000", 1.0: "#000000" } for node in tree.traverse(): nstyle = NodeStyle() nstyle["size"] = 0 if node.name in table: #print "Colouring individual " + node.name if args.colour_branches_by: nstyle["vt_line_color"] = colour_dict_br[table[node.name][ args.colour_branches_by]] # set branch colour nstyle["hz_line_color"] = colour_dict_br[table[node.name][ args.colour_branches_by]] if args.colour_backgrounds_by: if args.colour_branches_by in table[node.name]: if table[node.name][args.colour_branches_by] != "none": if not args.colour_branches_by: nstyle["hz_line_color"] = "black" nstyle["vt_line_color"] = "black" nstyle["bgcolor"] = colour_dict_bg[table[node.name][ args. colour_backgrounds_by]] # set background colour node.set_style(nstyle) else: # internal node descendants = node.get_leaves() descendant_labels_br = [] descendant_labels_bg = [] for d in descendants: if args.colour_branches_by: if d.name in table: this_label_br = table[d.name][ args.colour_branches_by] if this_label_br not in descendant_labels_br: descendant_labels_br.append(this_label_br) elif "none" not in descendant_labels_br: descendant_labels_br.append("none") if args.colour_backgrounds_by: if d.name in table: this_label_bg = table[d.name][ args.colour_backgrounds_by] if this_label_bg not in descendant_labels_bg: descendant_labels_bg.append(this_label_bg) elif "none" not in descendant_labels_bg: descendant_labels_bg.append("none") # nstyle = NodeStyle() # nstyle["size"] = 0 if len(descendant_labels_br ) == 1 and descendant_labels_br[0] != "none": this_colour = colour_dict_br[descendant_labels_br[0]] nstyle["vt_line_color"] = this_colour # set branch colour nstyle["hz_line_color"] = this_colour elif args.branch_support_colour and not node.is_leaf(): if int(node.support) in support_colours: nstyle["vt_line_color"] = support_colours[int( node.support)] # take colour from support value nstyle["hz_line_color"] = support_colours[int( node.support)] else: print " WARNING support values don't make sense. Note scale is assumed to be 0-1 unless using the --branch_support_percent flag." if len(descendant_labels_bg ) == 1 and descendant_labels_bg[0] != "none": this_colour = colour_dict_bg[descendant_labels_bg[0]] nstyle["bgcolor"] = this_colour # set background colour node.set_style(nstyle) if args.colour_nodes_by: if args.colour_nodes_by not in labels: print "- Colouring nodes by label " + args.colour_nodes_by colour_dict = getColourPalette(column_values[args.colour_nodes_by], args, args.colour_nodes_by) for node in tree.get_leaves(): if node.name in table: this_label = table[node.name][args.colour_nodes_by] this_colour = colour_dict[this_label] if this_colour != "None": node.img_style["fgcolor"] = this_colour node.img_style["size"] = args.node_size for node in tree.traverse(): node.img_style["hz_line_width"] = args.branch_thickness node.img_style["vt_line_width"] = args.branch_thickness # matches = search_by_size(tree, 75) # print("matches") # node = matches[0] # node.swap_children() ########### COMENTADO PARA VER COMO QUEDA CON EL BARCODE. PORQUE ESE NO TIENE TODOS LOS NODOS # rotate specific nodes # matches = search_by_size(tree, 463) # print("matches") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 601) # print("matches") # node = matches[0] # node.swap_children() # matches = search_by_size(node, 7) # print("matches") # node = matches[1] # node.swap_children() # matches = search_by_size(node, 5) # print("matches 5") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 8) # print("matches 8") # node = matches[5] # node.swap_children() # matches = search_by_size(tree, 349) # print("matches 349") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 192) # print("matches 192") # node = matches[1] # node.swap_children() # matches = search_by_size(tree, 182) # print("matches 182") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 180) # print("matches 180") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 175) # print("matches 175") # node = matches[0] # node.swap_children() # matches = search_by_size(tree, 34) # print("matches 34") # node = matches[0] # node.swap_children() #### FIN #### #for n in matches: # print n # set tree style ts = TreeStyle() ts.draw_guiding_lines = True ts.guiding_lines_color = 'black' if args.show_leaf_names: ts.show_leaf_name = True else: ts.show_leaf_name = False if args.length_scale: ts.scale = args.length_scale if args.branch_padding: ts.branch_vertical_margin = args.branch_padding if args.branch_support_print: ts.show_branch_support = True if args.fan: ts.mode = "c" print "\nPrinting circular tree (--fan)" else: print "\nPrinting rectangular tree, to switch to circular use --fan" if args.title: title = TextFace(args.title, fsize=20) title.margin_left = 20 title.margin_top = 20 ts.title.add_face(title, column=1) if args.no_guiding_lines: ts.draw_guiding_lines = False if args.data: print "\nPrinting data matrix as " + args.data_type + " with range (" + str( args.mindata) + "->" + str(args.maxdata) + ";" + str( args.centervalue) + "), height " + str( args.data_height) + ", width " + str(args.data_width) profileFace = ProfileFace(min_v=args.mindata, max_v=args.maxdata, center_v=args.centervalue, width=args.data_width, height=args.data_height, style=args.data_type) def mylayout(node): if node.is_leaf(): add_face_to_node(profileFace, node, 0, aligned=True) ts.layout_fn = mylayout # set root branch length to zero tree.dist = 0 if args.delete_branches: #print "Branches "+ args.delete_branches + " will not be shown" for branch in args.delete_branches: leaf = tree.get_leaves_by_name(branch)[0] #SRR1173284 leaf.delete() # render tree tree.render(args.output, w=args.width, dpi=400, units="mm", tree_style=ts) print "\n FINISHED! Tree plot printed to file " + args.output print if args.print_colour_dict: print colour_dict if args.colour_branches_by: print colour_dict_br if args.colour_backgrounds_by: print colour_dict_bg if args.interactive: print "\nEntering interactive mode..." tree.show(tree_style=ts)
def main(argv): treefilename = '' outfilename = '' database = 'test' usage = 'ColourTree.py -t <treefile> -o <outfile>' try: opts, args = getopt.getopt(argv,"ht:o:d:",["tree=","out=","db="]) if not opts: raise getopt.GetoptError('no opts') except getopt.GetoptError: print usage sys.exit(2) for opt, arg in opts: if opt == "-h": print usage sys.exit() elif opt in ("-t", "--tree"): treefilename = arg elif opt in ("-o", "--out"): outfilename = arg elif opt in ("-d", "--db"): database = arg tree = Tree(treefilename) if not outfilename: outfilename = treefilename.replace(".nwk", ".pdf") con = mdb.connect('localhost', 'root', '', database); with con: cur = con.cursor() for leaf in tree: name = leaf.name if name.find('KRAUS') > -1: color = 'Green' elif name.find('MOEL') > -1: color = 'Red' elif name.find('UNC') > -1: color = 'Orange' elif name.find('WILD') > -1: color = 'MediumBlue' else: cur.execute("Select Species.Genus, Species.Species FROM Species, Sequences WHERE Species.abbreviation = Sequences.species AND Sequences.seqid = %s", name) try: (genus, species) = cur.fetchone() leaf.name = '_'.join((genus[0], species, leaf.name)) except TypeError, e: print e continue if leaf.name.find('kraussiana') > -1: color = 'LightGreen' elif leaf.name.find('willdenowii') > -1: color = 'SteelBlue' else: color = 'Black' label = TextFace(leaf.name, fgcolor=color, fsize=16) leaf.add_face(label, column = 0, position="branch-right") leaf.add_face(TextFace(' '), column = 1, position="branch-right") name = '_'.join(name.split('_')[:-2]) try: cur.execute("SELECT vsd.leaf1, vsd.leaf2, vsd.leaf3, vsd.leaf4 FROM vsd, orfs WHERE vsd.gene_id = orfs.gene_id AND orfs.seqid = %s", name) vsd = cur.fetchone() cur.execute("SELECT normalized.leaf1, normalized.leaf2, normalized.leaf3, normalized.leaf4 FROM normalized, orfs WHERE normalized.gene_id = orfs.gene_id AND orfs.seqid = %s", name) normalized = cur.fetchone() for x in range(4): if vsd[x] == 'none': continue expression_label= TextFace(' %s ' % normalized[x], fsize=16) expression_label.background.color = get_colour(vsd[x]) expression_label.border.width = 1 expression_label.margin_left, expression_label.margin_right, expression_label.margin_top, expression_label.margin_bottom = 1,1,2,1 # This isn't working right : ( expression_label.border.width=1 leaf.add_face(expression_label, column = x+2, position="branch-right") except TypeError: continue draw_tree(tree, outfilename)
def plot_blast_result(tree_file, blast_result_file_list, id2description, id2mlst): ''' Projet Staph aureus PVL avec Laure Jaton Script pour afficher une phylog�nie et la conservation de facteurs de firulence c�te � c�te N�cessite r�sultats MLST, ensemble des r�sultats tblastn (facteurs de virulence vs chromosomes), ainsi qu'une correspondance entre les accession des g�nomes et les noms qu'on veut afficher dans la phylog�nie. Icemn pour les identifiants molis des patients, on les remplace par CHUV n. :param tree_file: phylog�nie au format newick avec identifiants correspondants � tous les dico utilis�s :param blast_result_file_list: r�sultats tblastn virulence factors vs chromosome (seulement best blast) :param id2description: identifiants g�nome utiis� dans l'arbre et description correspondante (i.e S aureus Newman) :param id2mlst: identitifiants arbre 2 S. aureus ST type :return: ''' blast2data = {} queries = [] for one_blast_file in blast_result_file_list: with open(one_blast_file, 'r') as f: for line in f: line = line.split('\t') if line[1] not in blast2data: blast2data[line[1]] = {} blast2data[line[1]][line[0]] = [float(line[2]), int(line[8]), int(line[9])] else: blast2data[line[1]][line[0]] = [float(line[2]), int(line[8]), int(line[9])] if line[0] not in queries: queries.append(line[0]) print blast2data print queries for one_blast in blast2data.keys(): for ref_gene in blast2data[one_blast].keys(): for query_gene in blast2data[one_blast].keys(): overlap = False if ref_gene == query_gene: continue if one_blast == 'NC_002745' and ref_gene == 'selm': print 'target:', ref_gene, blast2data[one_blast][ref_gene] print query_gene, blast2data[one_blast][query_gene] # check if position is overlapping try: sorted_coordinates = sorted(blast2data[one_blast][ref_gene][1:3]) if blast2data[one_blast][query_gene][1] <= sorted_coordinates[1] and blast2data[one_blast][query_gene][1]>= sorted_coordinates[0]: print 'Overlaping locations!' print one_blast, ref_gene, blast2data[one_blast][ref_gene] print one_blast, query_gene, blast2data[one_blast][query_gene] overlap =True sorted_coordinates = sorted(blast2data[one_blast][query_gene][1:3]) if blast2data[one_blast][ref_gene][1] <= sorted_coordinates[1] and blast2data[one_blast][ref_gene][1]>= sorted_coordinates[0]: print 'Overlapping locations!' print one_blast, ref_gene, blast2data[one_blast][ref_gene] print one_blast, query_gene, blast2data[one_blast][query_gene] overlap =True if overlap: if blast2data[one_blast][ref_gene][0] > blast2data[one_blast][query_gene][0]: del blast2data[one_blast][query_gene] print 'removing', query_gene else: del blast2data[one_blast][ref_gene] print 'removing', ref_gene break except KeyError: print 'colocation already resolved:', query_gene, ref_gene queries_count = {} for query in queries: queries_count[query] = 0 for one_blast in blast2data: if query in blast2data[one_blast]: queries_count[query]+=1 for query in queries_count: if queries_count[query] == 0: queries.pop(queries.index(query)) ''' rm_genes = ['selv','spsmA1','psmB1','psmB2','ses','set','sel','selX','sek','sel2','LukF', 'LukM', 'hly', 'hld' , 'hlgA', 'hlgB', 'hlgC', 'sed', 'sej', 'ser', 'selq1', 'sec3', 'sek2', 'seq2', 'lukD', 'lukE'] #rm_genes = ['icaR','icaA','icaB','icaC','icaD', 'sdrF', 'sdrH'] for gene in rm_genes: queries.pop(queries.index(gene)) ''' #queries = ['selv'] t1 = Tree(tree_file) #t.populate(8) # Calculate the midpoint node R = t1.get_midpoint_outgroup() t1.set_outgroup(R) t1.ladderize() #t2=t1 #for lf in t2.iter_leaves(): # try: # lf.name = ' %s (%s)' % (id2description[lf.name], id2mlst[lf.name]) # except: # #lf.name = ' %s (%s)' % (lf.name, lf.name) # # a = TextFace(' %s (%s)' % (lf.name, id2mlst[lf.name])) # a.fgcolor = "red" # lf.name = a #t2.render("test.svg", dpi=800, h=400) #import sys #sys.exit() # and set it as tree outgroup head = True for lf in t1.iter_leaves(): #lf.add_face(AttrFace("name", fsize=20), 0, position="branch-right") lf.branch_vertical_margin = 0 #data = [random.randint(0,2) for x in xrange(3)] for col, value in enumerate(sorted(queries)): print lf.name, value if head: 'first row, print gene names' #print 'ok!' n = TextFace(' %s ' % str(value)) n.margin_top = 4 n.margin_right = 4 n.margin_left = 4 n.margin_bottom = 4 n.inner_background.color = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") try: identity_value = blast2data[lf.name][value][0] if 'nord' in id2description[lf.name]: if float(identity_value) >70: if str(identity_value) == '100.00' or str(identity_value) == '100.0': identity_value = '100' else: identity_value = str(round(float(identity_value), 1)) n = TextFace(' %s ' % str(identity_value)) n.margin_top = 4 n.margin_right = 4 n.margin_left = 4 n.margin_bottom = 4 n.inner_background.color = rgb2hex(m.to_rgba(float(identity_value))) if float(identity_value) >92: n.fgcolor = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") else: identity_value = '-' n = TextFace(' %s ' % str(identity_value)) n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.inner_background.color = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") else: if float(identity_value) >70: if str(identity_value) == '100.00' or str(identity_value) == '100.0': identity_value = '100' else: identity_value = str(round(float(identity_value), 1)) n = TextFace(' %s ' % str(identity_value)) n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.inner_background.color = rgb2hex(m2.to_rgba(float(identity_value))) if float(identity_value) >92: n.fgcolor = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") else: identity_value = '-' n = TextFace(' %s ' % str(identity_value)) n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.inner_background.color = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") except KeyError: identity_value = '-' n = TextFace(' %s ' % str(identity_value)) n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.inner_background.color = "white" n.opacity = 1. lf.add_face(n, col, position="aligned") try: lf.name = ' %s (%s)' % (id2description[lf.name], id2mlst[lf.name]) except: #lf.name = ' %s (%s)' % (lf.name, lf.name) a = TextFace(' %s (%s)' % (lf.name, id2mlst[lf.name])) a.fgcolor = "red" lf.name = a head = False #.add_face(a, 0, position="aligned") # add boostrap suppot #for n in t1.traverse(): # if n.is_leaf(): # continue # n.add_face(TextFace(str(t1.support)), column=0, position = "branch-bottom") #ts = TreeStyle() #ts.show_branch_support = True # , tree_style=ts t1.render("test.svg", dpi=800, h=400)
def plot_blast_result(tree_file, blast_result_file_list, id2description, id2mlst, check_overlap, ordered_queries, fasta_file2accession, id_cutoff=80, reference_accession='-', accession2hit_filter=False, show_identity_values=True): ''' Projet Staph aureus PVL avec Laure Jaton Script pour afficher une phylogénie et la conservation de facteurs de virulence côte à côte Nécessite résultats MLST, ensemble des résultats tblastn (facteurs de virulence vs chromosomes), ainsi qu'une correspondance entre les accession des génomes et les noms qu'on veut afficher dans la phylogénie. Icemn pour les identifiants molis des patients, on les remplace par CHUV n. :param tree_file: phylogénie au format newick avec identifiants correspondants à tous les dico utilisés :param blast_result_file_list: résultats tblastn virulence factors vs chromosome (seulement best blast) :param id2description: identifiants génome utiisé dans l'arbre et description correspondante (i.e S aureus Newman) :param id2mlst: identitifiants arbre 2 S. aureus ST type :return: ''' import blast_utils blast2data, queries = blast_utils.remove_blast_redundancy( blast_result_file_list, check_overlap) queries_count = {} for query in queries: queries_count[query] = 0 for one_blast in blast2data: if query in blast2data[one_blast]: #print blast2data[one_blast][query] if float(blast2data[one_blast][query][0]) > id_cutoff: queries_count[query] += 1 else: del blast2data[one_blast][query] print queries_count for query in queries: print "Hit counts: %s\t%s" % (query, queries_count[query]) if queries_count[query] == 0: queries.pop(queries.index(query)) print 'delete columns with no matches ok' ''' rm_genes = ['selv','spsmA1','psmB1','psmB2','ses','set','sel','selX','sek','sel2','LukF', 'LukM', 'hly', 'hld' , 'hlgA', 'hlgB', 'hlgC', 'sed', 'sej', 'ser', 'selq1', 'sec3', 'sek2', 'seq2', 'lukD', 'lukE'] #rm_genes = ['icaR','icaA','icaB','icaC','icaD', 'sdrF', 'sdrH'] for gene in rm_genes: queries.pop(queries.index(gene)) ''' #queries = ['selv'] t1 = Tree(tree_file) tss = TreeStyle() #tss.show_branch_support = True # Calculate the midpoint node R = t1.get_midpoint_outgroup() t1.set_outgroup(R) t1.ladderize() ordered_queries_filtered = [] for query in ordered_queries: hit_count = 0 for lf2 in t1.iter_leaves(): try: accession = fasta_file2accession[lf2.name] tmpidentity = blast2data[accession][query][0] if float(tmpidentity) > float(id_cutoff): hit_count += 1 except: continue if hit_count > 0: ordered_queries_filtered.append(query) #print 'skippink-----------' head = True print 'drawing tree' print 'n initial queries: %s n kept: %s' % (len(ordered_queries), len(ordered_queries_filtered)) for lf in t1.iter_leaves(): #lf.add_face(AttrFace("name", fsize=20), 0, position="branch-right") lf.branch_vertical_margin = 0 #data = [random.randint(0,2) for x in xrange(3)] accession = fasta_file2accession[lf.name] for col, value in enumerate(ordered_queries_filtered): if head: if show_identity_values: #'first row, print gene names' #print 'ok!' n = TextFace(' %s ' % str(value)) n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.rotation = 270 n.vt_align = 2 n.hz_align = 2 n.inner_background.color = "white" n.opacity = 1. #lf.add_face(n, col, position="aligned") tss.aligned_header.add_face(n, col) else: n = TextFace(' %s ' % str(value), fsize=6) n.margin_top = 0 n.margin_right = 0 n.margin_left = 0 n.margin_bottom = 0 n.rotation = 270 n.vt_align = 2 n.hz_align = 2 n.inner_background.color = "white" n.opacity = 1. #lf.add_face(n, col, position="aligned") tss.aligned_header.add_face(n, col) try: identity_value = blast2data[accession][value][0] #print 'identity', lf.name, value, identity_value if lf.name != reference_accession: if not accession2hit_filter: # m_red color = rgb2hex(m_blue.to_rgba(float(identity_value))) else: # if filter, color hits that are not in the filter in green if accession in accession2hit_filter: if value in accession2hit_filter[accession]: # mred color = rgb2hex( m_green.to_rgba(float(identity_value))) else: color = rgb2hex( m_blue.to_rgba(float(identity_value))) else: color = rgb2hex( m_blue.to_rgba(float(identity_value))) else: # reference taxon, blue scale color = rgb2hex(m_blue.to_rgba(float(identity_value))) #if not show_identity_values: # color = rgb2hex(m_blue.to_rgba(float(identity_value))) except: identity_value = 0 color = "white" if show_identity_values: if float(identity_value) >= float(id_cutoff): if str(identity_value) == '100.00' or str( identity_value) == '100.0': identity_value = '100' n = TextFace("%s " % identity_value) else: # identity_value = str(round(float(identity_value), 1)) n = TextFace("%.2f" % round(float(identity_value), 2)) if float(identity_value) > 95: n.fgcolor = "white" n.opacity = 1. else: identity_value = '-' n = TextFace(' %s ' % str(identity_value)) n.opacity = 1. n.margin_top = 2 n.margin_right = 2 n.margin_left = 2 n.margin_bottom = 2 n.inner_background.color = color lf.add_face(n, col, position="aligned") else: if float(identity_value) >= float(id_cutoff): # don't show identity values n = TextFace(' ') n.margin_top = 0 n.margin_right = 0 n.margin_left = 0 n.margin_bottom = 0 #n.color = color n.inner_background.color = color lf.add_face(n, col, position="aligned") try: accession = fasta_file2accession[lf.name] lf.name = ' %s (%s)' % (id2description[accession], id2mlst[lf.name]) except KeyError: print '--------', id2description lf.name = ' %s (%s)' % (lf.name, id2mlst[lf.name]) head = False for n in t1.traverse(): nstyle = NodeStyle() if n.support < 0.9: #mundo = TextFace("%s" % str(n.support)) #n.add_face(mundo, column=1, position="branch-bottom") nstyle["fgcolor"] = "blue" nstyle["size"] = 6 n.set_style(nstyle) else: nstyle["fgcolor"] = "red" nstyle["size"] = 0 n.set_style(nstyle) print 'rendering tree' t1.render("profile.svg", dpi=1000, h=400, tree_style=tss)
def main(): args = parse_args() if args.data: print "\nReading tree from " + args.tree + " and data matrix from " + args.data tree = ClusterTree(args.tree, text_array=args.data) else: print "\nReading tree from " + args.tree tree = Tree(args.tree) if args.midpoint: R = tree.get_midpoint_outgroup() tree.set_outgroup(R) print "- Applying midpoint rooting" elif args.outgroup: tree.set_outgroup( tree&args.outgroup ) print "- Rooting using outgroup " + args.outgroup if not args.no_ladderize: tree.ladderize() print "- Ladderizing tree" table, column_list, column_values = readtable(args, tree.get_leaf_names()) labels = [] if args.labels: print "\nThese labels will be printed next to each strain:" for label in args.labels: if label in column_list: labels.append(label) print " " + label else: print "WARNING: specified label " + label + " was not found in the columns of the info file provided, " + args.info # set node styles # start by setting all to no shapes, black labels for n in tree.traverse(): nstyle = NodeStyle() nstyle["fgcolor"] = "black" nstyle["size"] = 0 n.set_style(nstyle) # add colour tags next to nodes if args.colour_tags: colour_tags = [] print "\nThese columns will be used to generate colour tags:" for label in args.colour_tags: if label in column_list: colour_tags.append(label) print " " + label else: print "\tWARNING: specified label for colour tagging, " + label + ", was not found in the columns of the info file provided, " + args.info for i in range(0,len(colour_tags)): label = colour_tags[i] colour_dict = getColourPalette(column_values[label],args,label) print "- Adding colour tag for " + label for node in tree.get_leaves(): this_face = Face() this_face.margin_left = args.padding node.add_face(this_face, column=0, position = "aligned") if node.name in table: this_label = table[node.name][label] this_colour = colour_dict[this_label] else: this_colour = "white" this_face = Face() this_face.background.color = this_colour this_face.margin_right = args.margin_right this_face.margin_left = args.margin_left this_face.margin_top = args.margin_top this_face.margin_bottom = args.margin_bottom this_face.border.width = args.border_width this_face.border.color="white" node.add_face(this_face, column=i+1, position = "aligned") print else: colour_tags = [] # add labels as columns for i in range(0,len(labels)): label = labels[i] print "- Adding label " + label if label == args.colour_nodes_by: print " also colouring nodes by these values" colour_dict = getColourPalette(column_values[label],args,label) for node in tree.get_leaves(): if node.name in table: this_label = table[node.name][label] this_colour = colour_dict[this_label] else: this_label = "" this_colour = "black" this_face = TextFace(text=this_label, fsize = args.font_size) if args.tags: this_face.background.color = this_colour elif label == args.colour_nodes_by: this_face.fgcolor = this_colour this_face.margin_right = args.padding if i == 0: this_face.margin_left = args.padding node.add_face(this_face, column=i+len(colour_tags)+1, position = "aligned") # set leaves to coloured circles node.img_style["size"] = args.node_size if label == args.colour_nodes_by: node.img_style["fgcolor"] = this_colour if args.colour_branches_by or args.colour_backgrounds_by or args.branch_support_colour: if args.colour_branches_by: print "- Colouring branches by label " + args.colour_branches_by colour_dict_br = getColourPalette(column_values[args.colour_branches_by],args,args.colour_branches_by) if args.colour_backgrounds_by: print "- Colouring node backgrounds by label " + args.colour_backgrounds_by colour_dict_bg = getColourPalette(column_values[args.colour_backgrounds_by],args,args.colour_backgrounds_by) if args.branch_support_colour: print "- Colouring branches by support values" # colours extracted from R using rgb( colorRamp(c("white","red", "black"))(seq(0, 1, length = 100)), max = 255) # support_colours = {0.0:"#FFFFFF",0.01:"#FFFFFF", 0.02:"#FFF9F9", 0.03:"#FFF4F4", 0.04:"#FFEFEF", 0.05:"#FFEAEA", 0.06:"#FFE5E5", 0.07:"#FFE0E0", 0.08:"#FFDADA", 0.09:"#FFD5D5", 0.1:"#FFD0D0", 0.11:"#FFCBCB", 0.12:"#FFC6C6", 0.13:"#FFC1C1", 0.14:"#FFBCBC", 0.15:"#FFB6B6", 0.16:"#FFB1B1", 0.17:"#FFACAC", 0.18:"#FFA7A7", 0.19:"#FFA2A2", 0.2:"#FF9D9D", 0.21:"#FF9797", 0.22:"#FF9292", 0.23:"#FF8D8D", 0.24:"#FF8888", 0.25:"#FF8383", 0.26:"#FF7E7E", 0.27:"#FF7979", 0.28:"#FF7373", 0.29:"#FF6E6E", 0.3:"#FF6969", 0.31:"#FF6464", 0.32:"#FF5F5F", 0.33:"#FF5A5A", 0.34:"#FF5454", 0.35:"#FF4F4F", 0.36:"#FF4A4A", 0.37:"#FF4545", 0.38:"#FF4040", 0.39:"#FF3B3B", 0.4:"#FF3636", 0.41:"#FF3030", 0.42:"#FF2B2B", 0.43:"#FF2626", 0.44:"#FF2121", 0.45:"#FF1C1C", 0.46:"#FF1717", 0.47:"#FF1212", 0.48:"#FF0C0C", 0.49:"#FF0707", 0.5:"#FF0202", 0.51:"#FC0000", 0.52:"#F70000", 0.53:"#F20000", 0.54:"#EC0000", 0.55:"#E70000", 0.56:"#E20000", 0.57:"#DD0000", 0.58:"#D80000", 0.59:"#D30000", 0.6:"#CE0000", 0.61:"#C80000", 0.62:"#C30000", 0.63:"#BE0000", 0.64:"#B90000", 0.65:"#B40000", 0.66:"#AF0000", 0.67:"#A90000", 0.68:"#A40000", 0.69:"#9F0000", 0.7:"#9A0000", 0.71:"#950000", 0.72:"#900000", 0.73:"#8B0000", 0.74:"#850000", 0.75:"#800000", 0.76:"#7B0000", 0.77:"#760000", 0.78:"#710000", 0.79:"#6C0000", 0.8:"#670000", 0.81:"#610000", 0.82:"#5C0000", 0.83:"#570000", 0.84:"#520000", 0.85:"#4D0000", 0.86:"#480000", 0.87:"#420000", 0.88:"#3D0000", 0.89:"#380000", 0.9:"#330000", 0.91:"#2E0000", 0.92:"#290000", 0.93:"#240000", 0.94:"#1E0000", 0.95:"#190000", 0.96:"#140000", 0.97:"#0F0000", 0.98:"#0A0000", 0.99:"#050000", 1:"#000000"} # rgb( colorRamp(c("red", "black"))(seq(0, 1, length = 100)), max = 255)) support_colours = {} if args.branch_support_cutoff: for i in range(0,args.branch_support_cutoff): support_colours[i] = "#FF0000" for i in range(args.branch_support_cutoff,101): support_colours[i] = "#000000" else: if args.branch_support_percent: support_colours = {0:"#FF0000",1:"#FF0000",2:"#FC0000",3:"#F90000",4:"#F70000",5:"#F40000",6:"#F20000",7:"#EF0000",8:"#EC0000",9:"#EA0000",10:"#E70000",11:"#E50000",12:"#E20000",13:"#E00000",14:"#DD0000",15:"#DA0000",16:"#D80000",17:"#D50000",18:"#D30000",19:"#D00000",20:"#CE0000",21:"#CB0000",22:"#C80000",23:"#C60000",24:"#C30000",25:"#C10000",26:"#BE0000",27:"#BC0000",28:"#B90000",29:"#B60000",30:"#B40000",31:"#B10000",32:"#AF0000",33:"#AC0000",34:"#AA0000",35:"#A70000",36:"#A40000",37:"#A20000",38:"#9F0000",39:"#9D0000",40:"#9A0000",41:"#970000",42:"#950000",43:"#920000",44:"#900000",45:"#8D0000",46:"#8B0000",47:"#880000",48:"#850000",49:"#830000",50:"#800000",51:"#7E0000",52:"#7B0000",53:"#790000",54:"#760000",55:"#730000",56:"#710000",57:"#6E0000",58:"#6C0000",59:"#690000",60:"#670000",61:"#640000",62:"#610000",63:"#5F0000",64:"#5C0000",65:"#5A0000",66:"#570000",67:"#540000",68:"#520000",69:"#4F0000",70:"#4D0000",71:"#4A0000",72:"#480000",73:"#450000",74:"#420000",75:"#400000",76:"#3D0000",77:"#3B0000",78:"#380000",79:"#360000",80:"#330000",81:"#300000",82:"#2E0000",83:"#2B0000",84:"#290000",85:"#260000",86:"#240000",87:"#210000",88:"#1E0000",89:"#1C0000",90:"#190000",91:"#170000",92:"#140000",93:"#120000",94:"#0F0000",95:"#0C0000",96:"#0A0000",97:"#070000",98:"#050000",99:"#020000",100:"#000000"} else: support_colours = {0.0:"#FF0000", 0.01:"#FF0000", 0.02:"#FC0000", 0.03:"#F90000", 0.04:"#F70000", 0.05:"#F40000", 0.06:"#F20000", 0.07:"#EF0000", 0.08:"#EC0000", 0.09:"#EA0000", 0.1:"#E70000", 0.11:"#E50000", 0.12:"#E20000", 0.13:"#E00000", 0.14:"#DD0000", 0.15:"#DA0000", 0.16:"#D80000", 0.17:"#D50000", 0.18:"#D30000", 0.19:"#D00000", 0.2:"#CE0000", 0.21:"#CB0000", 0.22:"#C80000", 0.23:"#C60000", 0.24:"#C30000", 0.25:"#C10000", 0.26:"#BE0000", 0.27:"#BC0000", 0.28:"#B90000", 0.29:"#B60000", 0.3:"#B40000", 0.31:"#B10000", 0.32:"#AF0000", 0.33:"#AC0000", 0.34:"#AA0000", 0.35:"#A70000", 0.36:"#A40000", 0.37:"#A20000", 0.38:"#9F0000", 0.39:"#9D0000", 0.4:"#9A0000", 0.41:"#970000", 0.42:"#950000", 0.43:"#920000", 0.44:"#900000", 0.45:"#8D0000", 0.46:"#8B0000", 0.47:"#880000", 0.48:"#850000", 0.49:"#830000", 0.5:"#800000", 0.51:"#7E0000", 0.52:"#7B0000", 0.53:"#790000", 0.54:"#760000", 0.55:"#730000", 0.56:"#710000", 0.57:"#6E0000", 0.58:"#6C0000", 0.59:"#690000", 0.6:"#670000", 0.61:"#640000", 0.62:"#610000", 0.63:"#5F0000", 0.64:"#5C0000", 0.65:"#5A0000", 0.66:"#570000", 0.67:"#540000", 0.68:"#520000", 0.69:"#4F0000", 0.7:"#4D0000", 0.71:"#4A0000", 0.72:"#480000", 0.73:"#450000", 0.74:"#420000", 0.75:"#400000", 0.76:"#3D0000", 0.77:"#3B0000", 0.78:"#380000", 0.79:"#360000", 0.8:"#330000", 0.81:"#300000", 0.82:"#2E0000", 0.83:"#2B0000", 0.84:"#290000", 0.85:"#260000", 0.86:"#240000", 0.87:"#210000", 0.88:"#1E0000", 0.89:"#1C0000", 0.9:"#190000", 0.91:"#170000", 0.92:"#140000", 0.93:"#120000", 0.94:"#0F0000", 0.95:"#0C0000", 0.96:"#0A0000", 0.97:"#070000", 0.98:"#050000", 0.99:"#020000", 1.0:"#000000"} for node in tree.traverse(): nstyle = NodeStyle() nstyle["size"] = 0 if node.name in table: #print "Colouring individual " + node.name if args.colour_branches_by: nstyle["vt_line_color"] = colour_dict_br[table[node.name][args.colour_branches_by]] # set branch colour nstyle["hz_line_color"] = colour_dict_br[table[node.name][args.colour_branches_by]] if args.colour_backgrounds_by: if args.colour_branches_by in table[node.name]: if table[node.name][args.colour_branches_by] != "none": nstyle["bgcolor"] = colour_dict_bg[table[node.name][args.colour_backgrounds_by]] # set background colour node.set_style(nstyle) else: # internal node descendants = node.get_leaves() descendant_labels_br = [] descendant_labels_bg = [] for d in descendants: if args.colour_branches_by: if d.name in table: this_label_br = table[d.name][args.colour_branches_by] if this_label_br not in descendant_labels_br: descendant_labels_br.append(this_label_br) elif "none" not in descendant_labels_br: descendant_labels_br.append("none") if args.colour_backgrounds_by: if d.name in table: this_label_bg = table[d.name][args.colour_backgrounds_by] if this_label_bg not in descendant_labels_bg: descendant_labels_bg.append(this_label_bg) elif "none" not in descendant_labels_bg: descendant_labels_bg.append("none") # nstyle = NodeStyle() # nstyle["size"] = 0 if len(descendant_labels_br) == 1 and descendant_labels_br[0] != "none": this_colour = colour_dict_br[descendant_labels_br[0]] nstyle["vt_line_color"] = this_colour # set branch colour nstyle["hz_line_color"] = this_colour elif args.branch_support_colour and not node.is_leaf(): if int(node.support) in support_colours: nstyle["vt_line_color"] = support_colours[int(node.support)] # take colour from support value nstyle["hz_line_color"] = support_colours[int(node.support)] else: print " WARNING support values don't make sense. Note scale is assumed to be 0-1 unless using the --branch_support_percent flag." if len(descendant_labels_bg) == 1 and descendant_labels_bg[0] != "none": this_colour = colour_dict_bg[descendant_labels_bg[0]] nstyle["bgcolor"] = this_colour # set background colour node.set_style(nstyle) if args.colour_nodes_by: if args.colour_nodes_by not in labels: print "- Colouring nodes by label " + args.colour_nodes_by colour_dict = getColourPalette(column_values[args.colour_nodes_by],args,args.colour_nodes_by) for node in tree.get_leaves(): if node.name in table: this_label = table[node.name][args.colour_nodes_by] this_colour = colour_dict[this_label] if this_colour != "None": node.img_style["fgcolor"] = this_colour node.img_style["size"] = args.node_size for node in tree.traverse(): node.img_style["hz_line_width"] = args.branch_thickness node.img_style["vt_line_width"] = args.branch_thickness # set tree style ts = TreeStyle() if args.show_leaf_names: ts.show_leaf_name = True else: ts.show_leaf_name = False if args.length_scale: ts.scale = args.length_scale if args.branch_padding: ts.branch_vertical_margin = args.branch_padding if args.branch_support_print: ts.show_branch_support = True if args.fan: ts.mode = "c" print "\nPrinting circular tree (--fan)" else: print "\nPrinting rectangular tree, to switch to circular use --fan" if args.title: title = TextFace(args.title, fsize=20) title.margin_left = 20 title.margin_top = 20 ts.title.add_face(title, column=1) if args.no_guiding_lines: ts.draw_guiding_lines = False if args.data: print "\nPrinting data matrix as " + args.data_type + " with range (" + str(args.mindata) + "->" + str(args.maxdata) + ";" + str(args.centervalue) + "), height " + str(args.data_height) + ", width " + str(args.data_width) profileFace = ProfileFace(min_v=args.mindata, max_v=args.maxdata, center_v=args.centervalue, width=args.data_width, height=args.data_height, style=args.data_type) def mylayout(node): if node.is_leaf(): add_face_to_node(profileFace, node, 0, aligned=True) ts.layout_fn = mylayout # set root branch length to zero tree.dist=0 # render tree tree.render(args.output, w=args.width, dpi=300, units="mm", tree_style=ts) print "\n FINISHED! Tree plot printed to file " + args.output print if args.print_colour_dict: print colour_dict if args.colour_branches_by: print colour_dict_br if args.colour_backgrounds_by: print colour_dict_bg if args.interactive: print "\nEntering interactive mode..." tree.show(tree_style=ts)