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)
#
# I borrowed some of this code from the ETE tutorial.
if options.datafile is not None:
array = t.arraytable
numcols = len(array.colNames)
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min+((matrix_max-matrix_min)/2)
# Max, Min, Center, Width, Height, Type)
# I give it 60 pixels per column by default
# (so that the width doesn't shrink down too much when we have more than a few columns)
# However, the user has the ability to change thsi if they need to / want to for larger data sets
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, width=numcols*options.data_width, height=35, style="heatmap")
for node in t.traverse():
if node.is_leaf():
node.add_face(profileFace, 1, position = "aligned")
# Add the color bar (kind of hacked in from matplotlib since there is no convenient way to get it from ETE)
# I could generate this in situ... for now I just have a file I like and run with it.
# This doesn't match exactlty becuase I don't have the time or motivation now to mess with QT to do it.
# It should be pretty close though...
from ete2 import ImgFace
imgloc = os.path.join(locateRootDirectory(), "src", "internal", "Colormap.png")
F1 = faces.TextFace("Minimum: %1.1f" %(matrix_min), ftype="Times", fsize=32 )
F2 = faces.ImgFace(imgloc)
F3 = faces.TextFace("%1.1f : Maximum" %(matrix_max), ftype="Times", fsize=32 )
ts.legend.add_face(F1, 0)
ts.legend.add_face(F2, 1)
#t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix)
t = ClusterTree("((A,B,C,D,E),(F,G,H));", text_array=matrix)
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 70, "cbars")
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
def plot_heat_tree(heatmap_file, tree_file, output_file=None):
'''
Plot heatmap next to a tree. The order of the heatmap **MUST** be the same,
as order of the leafs on the tree. The tree must be in the Newick format. If
*output_file* is specified, then heat-tree will be rendered as a PNG,
otherwise interactive browser will pop-up with your heat-tree.
Parameters
----------
heatmap_file: str
Path to the heatmap file. The first row must have '#Names' as first
element of the header.
e.g. #Names, A, B, C, D
row1, 2, 4, 0, 4
row2, 4, 6, 2, -1
tree_file: str
Path to the tree file in Newick format. The leaf node labels should
be the same as as row names in the heatmap file. E.g. row1, row2.
output_file: str, optional
If specified the heat-tree will be rendered in that file as a PNG image,
otherwise interactive browser will pop-up. **N.B.** program will wait
for you to exit the browser before continuing.
'''
import numpy
from ete2.treeview.faces import add_face_to_node
from ete2 import ClusterTree, TreeStyle, AttrFace, ProfileFace
# To operate with numbers efficiently
# Loads tree and array
t = ClusterTree(tree_file, heatmap_file)
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(matrix_max,
matrix_min,
matrix_avg,
1000,
14,
"heatmap",
colorscheme=2)
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
t.show(tree_style=ts)