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 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 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 drawTree(nwfile, outfile):
from ete2 import Tree, TreeStyle, TextFace
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = my_layout
ts.branch_vertical_margin = 12.75
ts.orientation = 1
titleFace = TextFace("Phylogenetic Tree", fsize=18, fgcolor="white")
titleFace.margin_top = 15
ts.title.add_face(titleFace, column=1)
t = Tree(nwfile)
t.render(outfile, tree_style=ts)
def drawTree(nwfile, outfile):
from ete2 import Tree, TreeStyle, TextFace
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = my_layout
ts.branch_vertical_margin = 12.75
ts.orientation = 1
titleFace = TextFace("Phylogenetic Tree", fsize=18, fgcolor="white")
titleFace.margin_top = 15
ts.title.add_face(titleFace, column=1)
t = Tree(nwfile)
t.render(outfile, tree_style=ts)
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 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)
