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