| 1 | # Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
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| 2 |
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| 3 | import json
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| 4 | import random
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| 5 | import math
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| 6 | import argparse
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| 7 |
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| 8 | TIME = "GENERATIONAL"
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| 9 | BALANCE = "MIN"
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| 10 |
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| 11 | # ------SVG---------
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| 12 | svg_file = 0
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| 13 |
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| 14 | svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.8"'
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| 15 | svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
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| 16 | svg_spine_line_style = 'stroke="rgb(0%,0%,80%)" stroke-width="2" stroke-opacity="1"'
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| 17 | #svg_spine_dot_style = 'r="3" stroke="black" stroke-width="0.4" fill="rgb(50%,50%,100%)"'
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| 18 | svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
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| 19 |
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| 20 | def svg_add_line(from_pos, to_pos, style=svg_line_style):
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| 21 | svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) + '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" />')
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| 22 |
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| 23 | def svg_add_dot(pos, style=svg_dot_style):
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| 24 | svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
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| 25 |
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| 26 | def svg_generate_line_style(percent):
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| 27 | # hotdog
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| 28 | from_col = [100, 70, 0]
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| 29 | to_col = [60, 0, 0]
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| 30 | # neon
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| 31 | # from_col = [30, 200, 255]
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| 32 | # to_col = [240, 0, 220]
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| 33 |
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| 34 | from_opa = 0.2
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| 35 | to_opa = 1.0
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| 36 | from_stroke = 1
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| 37 | to_stroke = 3
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| 38 |
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| 39 | opa = from_opa*(1-percent) + to_opa*percent
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| 40 | stroke = from_stroke*(1-percent) + to_stroke*percent
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| 41 |
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| 42 | percent = 1 - ((1-percent)**20)
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| 43 |
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| 44 | return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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| 45 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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| 46 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
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| 47 |
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| 48 | def svg_generate_dot_style(percent):
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| 49 | from_col = [100, 90, 0]
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| 50 | to_col = [60, 0, 0]
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| 51 | # neon
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| 52 | # from_col = [30, 200, 255]
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| 53 | # to_col = [240, 0, 220]
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| 54 |
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| 55 | from_opa = 0.2
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| 56 | to_opa = 1.0
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| 57 |
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| 58 | opa = from_opa*(1-percent) + to_opa*percent
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| 59 |
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| 60 | percent = 1 - ((1-percent)**20)
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| 61 |
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| 62 | return 'fill="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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| 63 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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| 64 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" r="1.5" stroke="black" stroke-width="0.2" fill-opacity="' + str(opa) + '" ' \
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| 65 | 'stroke-opacity="' + str(opa) + '"'
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| 66 |
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| 67 | # -------------------
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| 68 |
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| 69 | def load_data(dir):
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| 70 | global firstnode, nodes, inv_nodes
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| 71 | f = open(dir)
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| 72 | for line in f:
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| 73 | sline = line.split(' ', 2)
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| 74 | if len(sline) == 3:
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| 75 | if sline[1] == "[OFFSPRING]":
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| 76 | creature = json.loads(sline[2])
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| 77 | #print("B" +str(creature))
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| 78 | if "FromIDs" in creature:
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| 79 | assert(len(creature["FromIDs"]) == 1)
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| 80 | nodes[creature["ID"]] = creature["FromIDs"][0]
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| 81 | if not creature["FromIDs"][0] in nodes:
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| 82 | firstnode = creature["FromIDs"][0]
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| 83 | if "Time" in creature:
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| 84 | time[creature["ID"]] = creature["Time"]
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| 85 |
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| 86 | for k, v in sorted(nodes.items()):
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| 87 | inv_nodes[v] = inv_nodes.get(v, [])
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| 88 | inv_nodes[v].append(k)
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| 89 |
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| 90 |
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| 91 | def load_simple_data(dir):
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| 92 | global firstnode, nodes, inv_nodes
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| 93 | f = open(dir)
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| 94 | for line in f:
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| 95 | sline = line.split()
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| 96 | if len(sline) > 1:
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| 97 | #if int(sline[0]) > 15000:
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| 98 | # break
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| 99 | if sline[0] == firstnode:
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| 100 | continue
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| 101 | nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
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| 102 | else:
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| 103 | firstnode = sline[0]
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| 104 |
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| 105 | for k, v in sorted(nodes.items()):
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| 106 | inv_nodes[v] = inv_nodes.get(v, [])
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| 107 | inv_nodes[v].append(k)
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| 108 |
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| 109 | #print(str(inv_nodes))
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| 110 | #quit()
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| 111 |
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| 112 | def compute_depth(node):
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| 113 | my_depth = 0
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| 114 | if node in inv_nodes:
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| 115 | for c in inv_nodes[node]:
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| 116 | my_depth = max(my_depth, compute_depth(c)+1)
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| 117 | depth[node] = my_depth
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| 118 | return my_depth
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| 119 |
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| 120 | # ------------------------------------
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| 121 |
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| 122 | def xmin_crowd(x1, x2, y):
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| 123 | if BALANCE == "RANDOM":
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| 124 | return (x1 if random.randrange(2) == 0 else x2)
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| 125 | elif BALANCE == "MIN":
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| 126 | x1_closest = 999999
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| 127 | x2_closest = 999999
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| 128 | for pos in positions:
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| 129 | pos = positions[pos]
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| 130 | if pos[1] == y:
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| 131 | x1_closest = min(x1_closest, abs(x1-pos[0]))
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| 132 | x2_closest = min(x2_closest, abs(x2-pos[0]))
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| 133 | return (x1 if x1_closest > x2_closest else x2)
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| 134 | elif BALANCE == "DENSITY":
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| 135 | x1_dist = 0
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| 136 | x2_dist = 0
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| 137 | for pos in positions:
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| 138 | pos = positions[pos]
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| 139 | if pos[1] > y-10 or pos[1] < y+10:
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| 140 | dy = pos[1]-y
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| 141 | dx1 = pos[0]-x1
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| 142 | dx2 = pos[0]-x2
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| 143 |
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| 144 | x1_dist += math.sqrt(dy**2 + dx1**2)
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| 145 | x2_dist += math.sqrt(dy**2 + dx2**2)
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| 146 | return (x1 if x1_dist > x2_dist else x2)
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| 147 |
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| 148 | # ------------------------------------
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| 149 |
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| 150 | def prepos_children_reccurent(node):
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| 151 | for c in inv_nodes[node]:
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| 152 | #print(node + "->" + c)
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| 153 | dissimilarity = 0.5 #random.gauss(0,0.3)
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| 154 | if TIME == "BIRTHS":
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| 155 | id = ""
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| 156 | if c[0] == "c":
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| 157 | id = int(c[1:])
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| 158 | else:
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| 159 | id = int(c)
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| 160 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, id), id]
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| 161 | elif TIME == "GENERATIONAL":
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| 162 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, positions[node][1]+1), positions[node][1]+1]
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| 163 | elif TIME == "REAL":
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| 164 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, time[c]), time[c]]
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| 165 |
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| 166 | for c in inv_nodes[node]:
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| 167 | if c in inv_nodes:
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| 168 | prepos_children_reccurent(c)
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| 169 |
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| 170 | def prepos_children():
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| 171 | global max_height, max_width, min_width
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| 172 |
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| 173 | if not bool(time):
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| 174 | print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
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| 175 | TIME = "BIRTHS"
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| 176 |
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| 177 | positions[firstnode] = [0, 0]
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| 178 |
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| 179 | prepos_children_reccurent(firstnode)
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| 180 |
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| 181 | for pos in positions:
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| 182 | max_height = max(max_height, positions[pos][1])
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| 183 | max_width = max(max_width, positions[pos][0])
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| 184 | min_width = min(min_width, positions[pos][0])
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| 185 |
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| 186 | # ------------------------------------
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| 187 |
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| 188 | def draw_children_recurrent(node, max_depth):
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| 189 | global max_height, max_width, min_width
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| 190 | for c in inv_nodes[node]:
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| 191 | if c in inv_nodes:
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| 192 | draw_children_recurrent(c, max_depth)
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| 193 |
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| 194 | line_style = (svg_line_style if args.mono_tree else svg_generate_line_style(depth[c]/max_depth))
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| 195 | dot_style = (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[c]/max_depth))
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| 196 |
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| 197 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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| 198 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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| 199 | svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), dot_style)
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| 200 | def draw_children():
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| 201 | max_depth = 0
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| 202 | for k, v in depth.items():
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| 203 | max_depth = max(max_depth, v)
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| 204 | draw_children_recurrent(firstnode, max_depth)
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| 205 | dot_style = (svg_dot_style if args.mono_tree else svg_generate_dot_style(depth[firstnode]/max_depth))
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| 206 | svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), dot_style)
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| 207 |
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| 208 | def draw_spine_recurrent(node):
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| 209 | global max_height, max_width, min_width
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| 210 | for c in inv_nodes[node]:
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| 211 | if depth[c] == depth[node] - 1:
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| 212 | if c in inv_nodes:
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| 213 | draw_spine_recurrent(c)
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| 214 |
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| 215 | line_style = svg_spine_line_style
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| 216 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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| 217 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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| 218 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_dot_style)
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| 219 | def draw_spine():
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| 220 | draw_spine_recurrent(firstnode)
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| 221 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), svg_spine_dot_style)
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| 222 |
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| 223 | def draw_skeleton_reccurent(node, max_depth):
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| 224 | global max_height, max_width, min_width
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| 225 | for c in inv_nodes[node]:
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| 226 | if depth[c] >= min_skeleton_depth or depth[c] == max([depth[q] for q in inv_nodes[node]]):
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| 227 | if c in inv_nodes:
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| 228 | draw_skeleton_reccurent(c, max_depth)
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| 229 |
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| 230 | line_style = svg_spine_line_style
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| 231 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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| 232 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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| 233 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
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| 234 | # svg_spine_dot_style)
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| 235 | def draw_skeleton():
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| 236 | max_depth = 0
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| 237 | for k, v in depth.items():
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| 238 | max_depth = max(max_depth, v)
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| 239 |
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| 240 | draw_skeleton_reccurent(firstnode, max_depth)
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| 241 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
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| 242 | # svg_spine_dot_style)
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| 243 |
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| 244 |
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| 245 |
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| 246 | ##################################################### main #####################################################
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| 247 |
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| 248 | args = 0
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| 249 |
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| 250 | h = 800
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| 251 | w = 600
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| 252 | h_margin = 10
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| 253 | w_margin = 10
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| 254 | h_no_margs = h - 2* h_margin
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| 255 | w_no_margs = w - 2* w_margin
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| 256 |
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| 257 | max_height = 0
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| 258 | max_width = 0
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| 259 | min_width = 9999999999
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| 260 |
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| 261 | min_skeleton_depth = 0
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| 262 |
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| 263 | firstnode = ""
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| 264 | nodes = {}
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| 265 | inv_nodes = {}
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| 266 | positions = {}
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| 267 | depth = {}
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| 268 | time = {}
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| 269 |
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| 270 | def main():
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| 271 | global svg_file, min_skeleton_depth, args, TIME, BALANCE
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| 272 |
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| 273 | parser = argparse.ArgumentParser(description='Process some integers.')
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| 274 | parser.add_argument('--in', dest='input', required=True, help='input file with stuctured evolutionary data')
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| 275 | parser.add_argument('--out', dest='output', required=True, help='output file for the evolutionary tree')
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| 276 | draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
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| 277 | draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
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| 278 | draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
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| 279 |
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| 280 | draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
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| 281 | draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
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| 282 | draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
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| 283 |
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| 284 | draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
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| 285 | draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
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| 286 | draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
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| 287 |
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| 288 | #TODO: better names for those parameters
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| 289 | parser.add_argument('--time', default='BIRTHS', dest='time', help='values on vertical axis (REAL/GENERATIONAL)')
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| 290 | parser.add_argument('--balance', default='MIN',dest='balance', help='method of placing node in the tree (RANDOM/MIN/DENSITY)')
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| 291 |
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| 292 | mono_tree_parser = parser.add_mutually_exclusive_group(required=False)
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| 293 | mono_tree_parser.add_argument('--mono-tree', dest='mono_tree', action='store_true', help='whether the tree should be drawn with a single color')
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| 294 | mono_tree_parser.add_argument('--no-mono-tree', dest='mono_tree', action='store_false')
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| 295 |
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| 296 | parser.add_argument('--min-skeleton-depth', type=int, default=2, dest='min_skeleton_depth', help='minimal distance from the leafs for the nodes in the skeleton')
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| 297 | parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
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| 298 |
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| 299 | parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
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| 300 |
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| 301 | parser.set_defaults(mono_tree=False)
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| 302 | parser.set_defaults(draw_tree=True)
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| 303 | parser.set_defaults(draw_skeleton=False)
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| 304 | parser.set_defaults(draw_spine=False)
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| 305 |
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| 306 | parser.set_defaults(seed=-1)
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| 307 |
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| 308 | args = parser.parse_args()
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| 309 |
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| 310 | TIME = args.time
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| 311 | BALANCE = args.balance
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| 312 |
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| 313 | dir = args.input
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| 314 | min_skeleton_depth = args.min_skeleton_depth
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| 315 | seed = args.seed
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| 316 | if seed == -1:
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| 317 | seed = random.randint(0, 10000)
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| 318 | random.seed(seed)
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| 319 | print("seed:", seed)
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| 320 |
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| 321 | if args.simple_data:
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| 322 | load_simple_data(dir)
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| 323 | else:
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| 324 | load_data(dir)
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| 325 |
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| 326 | compute_depth(firstnode)
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| 327 |
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| 328 | svg_file = open(args.output, "w")
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| 329 | svg_file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
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| 330 | 'width="' + str(w) + '" height="' + str(h) + '">')
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| 331 |
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| 332 | prepos_children()
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| 333 |
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| 334 | if args.draw_tree:
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| 335 | draw_children()
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| 336 | if args.draw_skeleton:
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| 337 | draw_skeleton()
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| 338 | if args.draw_spine:
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| 339 | draw_spine()
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| 340 |
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| 341 | svg_file.write("</svg>")
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| 342 | svg_file.close()
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| 343 |
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| 344 | main()
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| 345 |
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