# Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
# Supports files generated by Framsticks experiments.
import json
import random
import math
import argparse
import time as ttime
TIME = "" # BIRTHS / GENERATIONAL / REAL
BALANCE = "" # MIN / DENSITY
DOT_STYLE = "" # NONE / NORMAL / CLEAR
JITTER = "" #
# ------SVG---------
svg_file = 0
svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.7"'
svg_mutation_line_style = 'stroke-width="1"'
svg_crossover_line_style = 'stroke-width="1"'
svg_spine_line_style = 'stroke="rgb(0%,90%,40%)" stroke-width="2" stroke-opacity="1"'
svg_scale_line_style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
svg_clear_dot_style = 'r="2" stroke="black" stroke-width="0.4" fill="none"'
svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
svg_scale_text_style = 'style="font-family: Arial; font-size: 12; fill: #000000;"'
def hex_to_style(hex):
default_style = ' stroke="black" stroke-opacity="0.5" '
if hex[0] == "#":
hex = hex[1:]
if len(hex) == 6 or len(hex) == 8:
try:
int(hex, 16)
except:
print("Invalid characters in the color's hex #" + hex + "! Assuming black.")
return default_style
red = 100*int(hex[0:2], 16)/255
green = 100*int(hex[2:4], 16)/255
blue = 100*int(hex[4:6], 16)/255
opacity = 0.5
if len(hex) == 8:
opacity = int(hex[6:8], 16)/255
return ' stroke="rgb(' +str(red)+ '%,' +str(green)+ '%,' +str(blue)+ '%)" stroke-opacity="' +str(opacity)+ '" '
else:
print("Invalid number of digits in the color's hex #" + hex + "! Assuming black.")
return default_style
def svg_add_line(from_pos, to_pos, style=svg_line_style):
svg_file.write('')
def svg_add_text(text, pos, anchor, style=svg_scale_text_style):
svg_file.write('' + text + '')
def svg_add_dot(pos, style=svg_dot_style):
svg_file.write('')
def svg_generate_line_style(percent):
# hotdog
from_col = [100, 70, 0]
to_col = [60, 0, 0]
# lava
# from_col = [100, 80, 0]
# to_col = [100, 0, 0]
# neon
# from_col = [30, 200, 255]
# to_col = [240, 0, 220]
from_opa = 0.2
to_opa = 1.0
from_stroke = 1
to_stroke = 3
opa = from_opa*(1-percent) + to_opa*percent
stroke = from_stroke*(1-percent) + to_stroke*percent
percent = 1 - ((1-percent)**20)
return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
+ str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
+ str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
def svg_generate_dot_style(kind):
kinds = ["red", "lawngreen", "royalblue", "magenta", "yellow", "cyan", "white", "black"]
r = min(2500/len(nodes), 10)
return 'fill="' + kinds[kind] + '" r="' + str(r) + '" stroke="black" stroke-width="' + str(r/10) + '" fill-opacity="1.0" ' \
'stroke-opacity="1.0"'
# -------------------
def load_data(dir):
global firstnode, nodes, inv_nodes, time
f = open(dir)
loaded = 0
for line in f:
sline = line.split(' ', 1)
if len(sline) == 2:
if sline[0] == "[OFFSPRING]":
creature = json.loads(sline[1])
#print("B" +str(creature))
if "FromIDs" in creature:
if not creature["ID"] in nodes:
nodes[creature["ID"]] = {}
# we assign to each parent its contribution to the genotype of the child
for i in range(0, len(creature["FromIDs"])):
inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
nodes[creature["ID"]][creature["FromIDs"][i]] = inherited
else:
print("Duplicated entry for " + creature["ID"])
quit()
if not creature["FromIDs"][0] in nodes and firstnode == None:
firstnode = creature["FromIDs"][0]
if "Time" in creature:
time[creature["ID"]] = creature["Time"]
if "Kind" in creature:
kind[creature["ID"]] = creature["Kind"]
loaded += 1
if loaded == max_nodes and max_nodes != 0:
break
for k, v in sorted(nodes.items()):
for val in sorted(v):
inv_nodes[val] = inv_nodes.get(val, [])
inv_nodes[val].append(k)
print(len(nodes))
def load_simple_data(dir):
global firstnode, nodes, inv_nodes
f = open(dir)
loaded = 0
for line in f:
sline = line.split()
if len(sline) > 1:
#if int(sline[0]) > 15000:
# break
if sline[0] == firstnode:
continue
nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
else:
firstnode = sline[0]
loaded += 1
if loaded == max_nodes and max_nodes != 0:
break
for k, v in sorted(nodes.items()):
inv_nodes[v] = inv_nodes.get(v, [])
inv_nodes[v].append(k)
#print(str(inv_nodes))
#quit()
def compute_depth(node):
my_depth = 0
if node in inv_nodes:
for c in inv_nodes[node]:
my_depth = max(my_depth, compute_depth(c)+1)
depth[node] = my_depth
return my_depth
# ------------------------------------
def xmin_crowd(x1, x2, y):
if BALANCE == "RANDOM":
return (x1 if random.randrange(2) == 0 else x2)
elif BALANCE == "MIN":
x1_closest = 999999
x2_closest = 999999
for pos in positions:
pos = positions[pos]
if pos[1] == y:
x1_closest = min(x1_closest, abs(x1-pos[0]))
x2_closest = min(x2_closest, abs(x2-pos[0]))
return (x1 if x1_closest > x2_closest else x2)
elif BALANCE == "DENSITY":
x1_dist = 0
x2_dist = 0
ymin = y-10
ymax = y+10
for pos in positions:
pos = positions[pos]
if pos[1] > ymin or pos[1] < ymax:
dysq = (pos[1]-y)**2
dx1 = pos[0]-x1
dx2 = pos[0]-x2
x1_dist += math.sqrt(dysq + dx1**2)
x2_dist += math.sqrt(dysq + dx2**2)
return (x1 if x1_dist > x2_dist else x2)
# ------------------------------------
def prepos_children():
global max_height, max_width, min_width, visited, TIME
print("firstnode " + firstnode)
if not bool(time):
print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
TIME = "BIRTHS"
positions[firstnode] = [0, 0]
#visited = {}
#visited[firstnode] = True
nodes_to_visit = [firstnode]
ccc = 0
timet = ttime.time()
while True:
ccc += 1
if ccc%1000 == 0 :
print(str(ccc) + " " + str(ttime.time()-timet))
timet = ttime.time()
current_node = nodes_to_visit[0]
if current_node in inv_nodes:
for c in inv_nodes[current_node]:
# we want to visit the node just once, after all of its parents
if c not in nodes_to_visit:
nodes_to_visit.append(c)
cy = 0
if TIME == "BIRTHS":
if c[0] == "c":
cy = int(c[1:])
else:
cy = int(c)
elif TIME == "GENERATIONAL":
cy = positions[current_node][1]+1
elif TIME == "REAL":
cy = time[c]
if len(nodes[c]) == 1:
dissimilarity = 0
if JITTER == True:
dissimilarity = random.gauss(0,1)
else:
dissimilarity = 1
positions[c] = [xmin_crowd(positions[current_node][0]-dissimilarity, positions[current_node][0]+dissimilarity, cy), cy]
else:
vsum = sum([v for k, v in nodes[c].items()])
cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
if JITTER == True:
positions[c] = [cx + random.gauss(0, 0.1), cy]
else:
positions[c] = [cx, cy]
#if c in inv_nodes:
# prepos_children_reccurent(c)
nodes_to_visit = nodes_to_visit[1:]
# if none left, we can stop
if len(nodes_to_visit) == 0:
break
# prepos_children_reccurent(firstnode)
for pos in positions:
max_height = max(max_height, positions[pos][1])
max_width = max(max_width, positions[pos][0])
min_width = min(min_width, positions[pos][0])
# ------------------------------------
def all_parents_visited(node):
apv = True
for k, v in sorted(nodes[node].items()):
if not k in visited:
apv = False
break
return apv
# ------------------------------------
def draw_children():
max_depth = 0
for k, v in depth.items():
max_depth = max(max_depth, v)
nodes_to_visit = [firstnode]
while True:
current_node = nodes_to_visit[0]
if current_node in inv_nodes:
for c in inv_nodes[current_node]: # inv_node => p->c
if not c in nodes_to_visit:
nodes_to_visit.append(c)
line_style = ""
if COLORING == "NONE":
line_style = svg_line_style
elif COLORING == "TYPE":
line_style = (svg_mutation_line_style if len(nodes[c]) == 1 else svg_crossover_line_style)
else: # IMPORTANCE, default
line_style = svg_generate_line_style(depth[c]/max_depth)
svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
(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)
# we want to draw the node just once
if DOT_STYLE == "NONE":
continue
elif DOT_STYLE == "TYPE":
dot_style = svg_generate_dot_style(kind[current_node] if current_node in kind else 0) #type
else: # NORMAL, default
dot_style = svg_clear_dot_style #svg_generate_dot_style(depth[c]/max_depth)
svg_add_dot( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height), dot_style)
#svg_add_text( str(depth[current_node]), (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width),
# h_margin+h_no_margs*positions[current_node][1]/max_height), "end")
# we remove the current node from the list
nodes_to_visit = nodes_to_visit[1:]
# if none left, we can stop
if len(nodes_to_visit) == 0:
break
def draw_spine():
nodes_to_visit = [firstnode]
while True:
current_node = nodes_to_visit[0]
if current_node in inv_nodes:
for c in inv_nodes[current_node]: # inv_node => p->c
if depth[c] == depth[current_node] - 1:
if not c in nodes_to_visit:
nodes_to_visit.append(c)
line_style = svg_spine_line_style
svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
(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)
# we remove the current node from the list
nodes_to_visit = nodes_to_visit[1:]
# if none left, we can stop
if len(nodes_to_visit) == 0:
break
def draw_skeleton():
nodes_to_visit = [firstnode]
while True:
current_node = nodes_to_visit[0]
if current_node in inv_nodes:
for c in inv_nodes[current_node]: # inv_node => p->c
if depth[c] >= min_skeleton_depth:
if not c in nodes_to_visit:
nodes_to_visit.append(c)
line_style = svg_spine_line_style
svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
(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)
# we remove the current node from the list
nodes_to_visit = nodes_to_visit[1:]
# if none left, we can stop
if len(nodes_to_visit) == 0:
break
# ------------------------------------
def draw_scale(filename ,type):
svg_add_text("Generated from " + filename.split("\\")[-1], (5, 15), "start")
svg_add_line( (w*0.7, h_margin), (w, h_margin), svg_scale_line_style)
start_text = ""
if TIME == "BIRTHS":
start_text = "Birth #" + str(min([int(k[1:]) for k, v in nodes.items()]))
if TIME == "REAL":
start_text = "Time " + str(min([v for k, v in time.items()]))
if TIME == "GENERATIONAL":
start_text = "Depth " + str(min([v for k, v in depth.items()]))
svg_add_text( start_text, (w, h_margin + 15), "end")
svg_add_line( (w*0.7, h-h_margin), (w, h-h_margin), svg_scale_line_style)
end_text = ""
if TIME == "BIRTHS":
end_text = "Birth #" + str(max([int(k[1:]) for k, v in nodes.items()]))
if TIME == "REAL":
end_text = "Time " + str(max([v for k, v in time.items()]))
if TIME == "GENERATIONAL":
end_text = "Depth " + str(max([v for k, v in depth.items()]))
svg_add_text( end_text, (w, h-h_margin + 15), "end")
##################################################### main #####################################################
args = 0
h = 800
w = 600
h_margin = 20
w_margin = 10
h_no_margs = h - 2* h_margin
w_no_margs = w - 2* w_margin
max_height = 0
max_width = 0
min_width = 9999999999
min_skeleton_depth = 0
max_nodes = 0
firstnode = None
nodes = {}
inv_nodes = {}
positions = {}
visited= {}
depth = {}
time = {}
kind = {}
def main():
global svg_file, min_skeleton_depth, max_nodes, args, \
TIME, BALANCE, DOT_STYLE, COLORING, JITTER, \
svg_mutation_line_style, svg_crossover_line_style
parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship information from a text file. Supports files generated by Framsticks experiments.')
parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG format)')
draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
#TODO: better names for those parameters
parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL(d)/REAL); '
'BIRTHS: time measured as the number of births since the beginning; '
'GENERATIONAL: time measured as number of ancestors; '
'REAL: real time of the simulation')
parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY(d))')
parser.add_argument('-s', '--scale', default='NONE', dest='scale', help='type of timescale added to the tree (NONE(d)/SIMPLE)')
parser.add_argument('-c', '--coloring', default='IMPORTANCE', dest="coloring", help='method of coloring the tree (NONE/IMPORTANCE(d)/TYPE)')
parser.add_argument('-d', '--dots', default='TYPE', dest='dots', help='method of drawing dots (individuals) (NONE/NORMAL/TYPE(d))')
parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
parser.add_argument('--color-mut', default="#000000", dest="color_mut", help='color of clone/mutation lines in rgba (e.g. #FF60B240) for TYPE coloring')
parser.add_argument('--color-cross', default="#660198", dest="color_cross", help='color of crossover lines in rgba (e.g. #FF60B240) for TYPE coloring')
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')
parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
parser.add_argument('-x', '--max-nodes', type=int, default=0, dest='max_nodes', help='maximum number of nodes drawn (starting from the first one)')
parser.set_defaults(draw_tree=True)
parser.set_defaults(draw_skeleton=False)
parser.set_defaults(draw_spine=False)
parser.set_defaults(seed=-1)
args = parser.parse_args()
TIME = args.time.upper()
BALANCE = args.balance.upper()
DOT_STYLE = args.dots.upper()
COLORING = args.coloring.upper()
SCALE = args.scale.upper()
JITTER = args.jitter
if not TIME in ['BIRTHS', 'GENERATIONAL', 'REAL']\
or not BALANCE in ['RANDOM', 'MIN', 'DENSITY']\
or not DOT_STYLE in ['NONE', 'NORMAL', 'TYPE']\
or not COLORING in ['NONE', 'IMPORTANCE', 'TYPE']\
or not SCALE in ['NONE', 'SIMPLE']:
print("Incorrect value of one of the parameters! Closing the program.") #TODO don't be lazy, figure out which parameter is wrong...
return
svg_mutation_line_style += hex_to_style(args.color_mut)
svg_crossover_line_style += hex_to_style(args.color_cross)
dir = args.input
min_skeleton_depth = args.min_skeleton_depth
max_nodes = args.max_nodes
seed = args.seed
if seed == -1:
seed = random.randint(0, 10000)
random.seed(seed)
print("seed:", seed)
if args.simple_data:
load_simple_data(dir)
else:
load_data(dir)
compute_depth(firstnode)
svg_file = open(args.output, "w")
svg_file.write('")
svg_file.close()
main()