A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ print "Example numerical matrix" print matrix # #Names col1 col2 col3 col4 col5 col6 col7 # A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58 # B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12 # C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36 # D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93 # E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65 # F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48 # G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26 # H -1.53 -1.25 0.59 -0.30 0.32 1.41 0.77 # # # We load a tree structure whose leaf nodes correspond to rows in the # numerical matrix. We use the text_array argument to link the tree # with numerical matrix. t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) t.show("heatmap") t.show("cluster_cbars") t.show("cluster_bars") t.show("cluster_lines")
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)
print matrix # #Names col1 col2 col3 col4 col5 col6 col7 # A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58 # B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12 # C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36 # D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93 # E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65 # F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48 # G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26 # H -1.53 -1.25 0.59 -0.30 0.32 1.41 0.77 # # # We load a tree structure whose leaf nodes correspond to rows in the # numerical matrix. We use the text_array argument to link the tree # with numerical matrix. t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) print "Example tree", t # /-A # /--------| # | \-B # /--------| # | | /-C # | \--------| # | | /-D #---------| \--------| # | \-E # | # | /-F # \--------| # | /-G # \--------|
from ete2 import ClusterTree, TreeStyle import scipy.cluster.hierarchy as sch import scipy.spatial.distance import matplotlib.pyplot as plt import numpy as np from itertools import combinations from scipy.spatial.distance import pdist from scipy.spatial import distance_matrix #https://en.wikipedia.org/wiki/Newick_format #The tree, in string format (the corresponding graph is drawn in the image/NewickExample.png) tree = ClusterTree('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);') #Distance matrix for this example is: #distance_matrix= # [[0.0, 0.3, 0.9, 1.0], # [0.3, 0.0, 1.0, 1.1], # [0.9, 1.0, 0.0, 0.7], # [1.0, 1.1, 0.1, 0.0]] #the distance_matrix can be easlily made up by the following lines: data=[ [0.1],[0.2],[0.3],[0.4],[0.5] ] #print distance_matrix(data,data) #the linkage matrix can be easlily made up by the following lines: #print pdist(data) leaves = tree.get_leaf_names() ts = TreeStyle() ts.show_leaf_name=True ts.show_branch_length=True
#t = ClusterTree(PATH+"diauxic.nw", PATH+"diauxic.array") matrix = """ #Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7 A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ #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")
for c in reversed(gradient(COLOR2)): color = QtGui.QColor(c) colors.append(color) return colors # ==================================== # JUST A TEST SCRIPT # ==================================== from ete2 import ClusterTree, ProfileFace # Let's replace the function that generates the color gradients in # ProfileFaces, so the config is applied in all profile faces. ProfileFace.get_color_gradient = get_color_gradient # Test it with a clustering tree! matrix = """ #Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7 A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) t.show("heatmap")
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)
color=QtGui.QColor(c) colors.append(color) return colors # ==================================== # JUST A TEST SCRIPT # ==================================== from ete2 import ClusterTree, ProfileFace # Let's replace the function that generates the color gradients in # ProfileFaces, so the config is applied in all profile faces. ProfileFace.get_color_gradient = get_color_gradient # Test it with a clustering tree! matrix = """ #Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7 A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) t.show("heatmap")
matrix = """ #Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7 A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ #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")
#################################### # Import lots of stuff for drawing... #################################### from ete2 import Tree, faces, TreeStyle, NodeStyle, AttrFace, ClusterTree, ProfileFace import fileinput import sqlite3 from TreeFuncs import * # Read Newick file sys.stderr.write("Reading tree file...\n") if options.datafile is None: t = Tree(args[0]) else: t = ClusterTree(args[0], options.datafile) # If outgroup is specified, re-root now before doing anything else. # This will just fail if the specified protein isn't present in the tree. t = rerootEteTree(t, root_leaf = options.rootgene, root_leaf_part = options.rootorg) ############################################## # Get various gene / organism / annotation / neighborhood / cluster info out of the database ############################################## # Annotation and organism geneToAnnote = {} geneToOrganism = {} sys.stderr.write("Reading gene annotations and organisms from database...\n") # FIXME - This should call the library functions to get geneinfo for specific sets of genes
E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ print "Example numerical matrix" #print matrix # #Names col1 col2 col3 col4 col5 col6 col7 # A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58 # B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12 # C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36 # D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93 # E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65 # F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48 # G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26 # H -1.53 -1.25 0.59 -0.30 0.32 1.41 0.77 # # # We load a tree structure whose leaf nodes correspond to rows in the # numerical matrix. We use the text_array argument to link the tree # with numerical matrix. t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) print t.children[0].children[0] print t.children[0].children[0].get_silhouette() #print t.get_silhouette() #t.show("heatmap") #t.show("cluster_cbars") #t.show("cluster_bars") t.show("cluster_lines")
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)
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)
from ete2 import ClusterTree, faces # To operate with numbersd bub efficiently import numpy PATH = "./" # Loads tree and array t = ClusterTree(PATH+"diauxic.nw", PATH+"diauxic.array") # nodes are linked to the array table array = t.arraytable # Calculates some stats on the matrix 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 = faces.ProfileFace(matrix_max, matrix_min, matrix_avg, \ 200, 14, "heatmap") cbarsFace = faces.ProfileFace(matrix_max,matrix_min,matrix_avg,200,70,"cbars") nameFace = faces.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 faces.add_face_to_node(profileFace, node, 0, aligned=True)