genome_diversity: dpmix_plot.py annotate

annotate dpmix_plot.py @ 35:ea52b23f1141

Bug fixes for Draw variants, Phylip, and gd_d_tools

author	Richard Burhans <burhans@bx.psu.edu>
date	Wed, 20 Nov 2013 13:46:10 -0500
parents	a631c2f6d913
children

rev	line source
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	1 #!/usr/bin/env python
4b6590dd7250 Uploaded miller-lab parents: diff changeset	2
4b6590dd7250 Uploaded miller-lab parents: diff changeset	3 import os
4b6590dd7250 Uploaded miller-lab parents: diff changeset	4 import sys
4b6590dd7250 Uploaded miller-lab parents: diff changeset	5 import math
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	6
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	7 import matplotlib as mpl
4b6590dd7250 Uploaded miller-lab parents: diff changeset	8 mpl.use('PDF')
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	9 from matplotlib.backends.backend_pdf import PdfPages
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	10 import matplotlib.pyplot as plt
4b6590dd7250 Uploaded miller-lab parents: diff changeset	11 from matplotlib.path import Path
4b6590dd7250 Uploaded miller-lab parents: diff changeset	12 import matplotlib.patches as patches
4b6590dd7250 Uploaded miller-lab parents: diff changeset	13
4b6590dd7250 Uploaded miller-lab parents: diff changeset	14 ################################################################################
4b6590dd7250 Uploaded miller-lab parents: diff changeset	15
4b6590dd7250 Uploaded miller-lab parents: diff changeset	16 def build_chrom_len_dict(dbkey, galaxy_data_index_dir):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	17 chrom_len_root = os.path.join(galaxy_data_index_dir, 'shared/ucsc/chrom')
4b6590dd7250 Uploaded miller-lab parents: diff changeset	18 chrom_len_file = '{0}.len'.format(dbkey)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	19 chrom_len_path = os.path.join(chrom_len_root, chrom_len_file)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	20
4b6590dd7250 Uploaded miller-lab parents: diff changeset	21 chrom_len = {}
4b6590dd7250 Uploaded miller-lab parents: diff changeset	22
4b6590dd7250 Uploaded miller-lab parents: diff changeset	23 try:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	24 with open(chrom_len_path) as fh:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	25 for line in fh:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	26 line = line.rstrip('\r\n')
4b6590dd7250 Uploaded miller-lab parents: diff changeset	27 elems = line.split()
4b6590dd7250 Uploaded miller-lab parents: diff changeset	28 if len(elems) == 2:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	29 chrom = elems[0]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	30 length = int(elems[1])
4b6590dd7250 Uploaded miller-lab parents: diff changeset	31 chrom_len[chrom] = length
4b6590dd7250 Uploaded miller-lab parents: diff changeset	32 except:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	33 pass
4b6590dd7250 Uploaded miller-lab parents: diff changeset	34
4b6590dd7250 Uploaded miller-lab parents: diff changeset	35 return chrom_len
4b6590dd7250 Uploaded miller-lab parents: diff changeset	36
4b6590dd7250 Uploaded miller-lab parents: diff changeset	37 def parse_input_file(input_file):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	38 chroms = []
4b6590dd7250 Uploaded miller-lab parents: diff changeset	39 individuals = []
4b6590dd7250 Uploaded miller-lab parents: diff changeset	40 data = {}
4b6590dd7250 Uploaded miller-lab parents: diff changeset	41 chrom_len = {}
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	42 used_states = []
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	43
4b6590dd7250 Uploaded miller-lab parents: diff changeset	44 with open(input_file) as fh:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	45 for line in fh:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	46 line = line.strip()
4b6590dd7250 Uploaded miller-lab parents: diff changeset	47 if line:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	48 elems = line.split()
4b6590dd7250 Uploaded miller-lab parents: diff changeset	49 chrom = elems[0]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	50 p1, p2, state = map(int, elems[1:4])
4b6590dd7250 Uploaded miller-lab parents: diff changeset	51 id = elems[4]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	52
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	53 if state not in used_states:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	54 used_states.append(state)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	55
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	56 if chrom not in chroms:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	57 chroms.append(chrom)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	58
4b6590dd7250 Uploaded miller-lab parents: diff changeset	59 if id not in individuals:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	60 individuals.append(id)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	61
4b6590dd7250 Uploaded miller-lab parents: diff changeset	62 data.setdefault(chrom, {})
4b6590dd7250 Uploaded miller-lab parents: diff changeset	63 data[chrom].setdefault(id, [])
4b6590dd7250 Uploaded miller-lab parents: diff changeset	64 data[chrom][id].append((p1, p2, state))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	65
4b6590dd7250 Uploaded miller-lab parents: diff changeset	66 if p2 > chrom_len.setdefault(chrom, 0):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	67 chrom_len[chrom] = p2
4b6590dd7250 Uploaded miller-lab parents: diff changeset	68
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	69 return chroms, individuals, data, chrom_len, used_states
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	70
4b6590dd7250 Uploaded miller-lab parents: diff changeset	71 def check_chroms(chroms, chrom_len, dbkey):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	72 error = 0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	73 for chrom in chroms:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	74 if chrom not in chrom_len:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	75 print >> sys.stderr, "Can't find length for {0} chromosome {1}".format(dbkey, chrom)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	76 error = 1
4b6590dd7250 Uploaded miller-lab parents: diff changeset	77 if error:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	78 sys.exit(1)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	79
4b6590dd7250 Uploaded miller-lab parents: diff changeset	80 def check_data(data, chrom_len, dbkey):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	81 error = 0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	82 for chrom in data:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	83 chrom_beg = 0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	84 chrom_end = chrom_len[chrom]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	85 for individual in data[chrom]:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	86 for p1, p2, state in data[chrom][individual]:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	87 if p1 >= p2:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	88 print >> sys.stderr, "Bad data line: begin >= end: {0} {1} {2} {3}".format(chrom, p1, p2, state, individual)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	89 error = 1
4b6590dd7250 Uploaded miller-lab parents: diff changeset	90 if p1 < chrom_beg or p2 > chrom_end:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	91 print >> sys.stderr, "Bad data line: outside {0} boundaries[{1} - {2}]: {3} {4} {5} {6}".format(dbkey, chrom_beg, chrom_end, chrom, p1, p2, state, individual)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	92 error = 1
4b6590dd7250 Uploaded miller-lab parents: diff changeset	93 if error:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	94 sys.exit(1)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	95
4b6590dd7250 Uploaded miller-lab parents: diff changeset	96 def make_rectangle(p1, p2, color, bottom=0.0, top=1.0):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	97 verts = [
4b6590dd7250 Uploaded miller-lab parents: diff changeset	98 (p1, bottom), # left, bottom
4b6590dd7250 Uploaded miller-lab parents: diff changeset	99 (p1, top), # left, top
4b6590dd7250 Uploaded miller-lab parents: diff changeset	100 (p2, top), # right, top
4b6590dd7250 Uploaded miller-lab parents: diff changeset	101 (p2, bottom), # right, bottom
4b6590dd7250 Uploaded miller-lab parents: diff changeset	102 (0.0, 0.0) # ignored
4b6590dd7250 Uploaded miller-lab parents: diff changeset	103 ]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	104
4b6590dd7250 Uploaded miller-lab parents: diff changeset	105 codes = [
4b6590dd7250 Uploaded miller-lab parents: diff changeset	106 Path.MOVETO,
4b6590dd7250 Uploaded miller-lab parents: diff changeset	107 Path.LINETO,
4b6590dd7250 Uploaded miller-lab parents: diff changeset	108 Path.LINETO,
4b6590dd7250 Uploaded miller-lab parents: diff changeset	109 Path.LINETO,
4b6590dd7250 Uploaded miller-lab parents: diff changeset	110 Path.CLOSEPOLY
4b6590dd7250 Uploaded miller-lab parents: diff changeset	111 ]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	112
4b6590dd7250 Uploaded miller-lab parents: diff changeset	113 path = Path(verts, codes)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	114 return patches.PathPatch(path, facecolor=color, lw=0)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	115
4b6590dd7250 Uploaded miller-lab parents: diff changeset	116 def make_split_rectangle(p1, p2, top_color, bottom_color):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	117 patch1 = make_rectangle(p1, p2, bottom_color, top=0.5)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	118 patch2 = make_rectangle(p1, p2, top_color, bottom=0.5)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	119 return [patch1, patch2]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	120
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	121 def make_state_rectangle_2pop(p1, p2, state, chrom, individual):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	122 p1_color = 'r'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	123 p2_color = 'g'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	124 heterochromatin_color = '#c7c7c7'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	125
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	126 if state == 0:
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	127 return [ make_rectangle(p1, p2, heterochromatin_color) ]
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	128 elif state == 1:
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	129 return [ make_rectangle(p1, p2, p1_color) ]
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	130 elif state == 2:
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	131 return [ make_rectangle(p1, p2, p2_color) ]
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	132 elif state == 3:
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	133 return make_split_rectangle(p1, p2, p1_color, p2_color)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	134 else:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	135 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	136 sys.exit(1)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	137
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	138 def make_state_rectangle_3pop(p1, p2, state, chrom, individual):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	139 p1_color = 'r'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	140 p2_color = 'g'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	141 p3_color = 'b'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	142 heterochromatin_color = '#c7c7c7'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	143
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	144 if state == 0:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	145 return [ make_rectangle(p1, p2, heterochromatin_color) ]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	146 if state == 1:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	147 return [ make_rectangle(p1, p2, p1_color) ]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	148 if state == 2:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	149 return [ make_rectangle(p1, p2, p2_color) ]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	150 if state == 3:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	151 return [ make_rectangle(p1, p2, p3_color) ]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	152 if state == 4:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	153 return make_split_rectangle(p1, p2, p1_color, p2_color)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	154 if state == 5:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	155 return make_split_rectangle(p1, p2, p1_color, p3_color)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	156 if state == 6:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	157 return make_split_rectangle(p1, p2, p2_color, p3_color)
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	158 else:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	159 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	160 sys.exit(1)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	161
4b6590dd7250 Uploaded miller-lab parents: diff changeset	162 def nicenum(num, round=False):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	163 if num == 0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	164 return 0.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	165
4b6590dd7250 Uploaded miller-lab parents: diff changeset	166 exp = int(math.floor(math.log10(num)))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	167 f = num / math.pow(10, exp)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	168
4b6590dd7250 Uploaded miller-lab parents: diff changeset	169 if round:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	170 if f < 1.5:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	171 nf = 1.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	172 elif f < 3.0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	173 nf = 2.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	174 elif f < 7.0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	175 nf = 5.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	176 else:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	177 nf = 10.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	178 else:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	179 if f <= 1.0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	180 nf = 1.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	181 elif f <= 2.0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	182 nf = 2.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	183 elif f <= 5.0:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	184 nf = 5.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	185 else:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	186 nf = 10.0
4b6590dd7250 Uploaded miller-lab parents: diff changeset	187
4b6590dd7250 Uploaded miller-lab parents: diff changeset	188 return nf * pow(10, exp)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	189
4b6590dd7250 Uploaded miller-lab parents: diff changeset	190 def tick_foo(beg, end, loose=False):
4b6590dd7250 Uploaded miller-lab parents: diff changeset	191 ntick = 10
4b6590dd7250 Uploaded miller-lab parents: diff changeset	192
4b6590dd7250 Uploaded miller-lab parents: diff changeset	193 range = nicenum(end - beg, round=False)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	194 d = nicenum(range/(ntick - 1), round=True)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	195 digits = int(math.floor(math.log10(d)))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	196
4b6590dd7250 Uploaded miller-lab parents: diff changeset	197 if loose:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	198 graph_min = math.floor(beg/d) * d
4b6590dd7250 Uploaded miller-lab parents: diff changeset	199 graph_max = math.ceil(end/d) * d
4b6590dd7250 Uploaded miller-lab parents: diff changeset	200 else:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	201 graph_min = beg
4b6590dd7250 Uploaded miller-lab parents: diff changeset	202 graph_max = end
4b6590dd7250 Uploaded miller-lab parents: diff changeset	203
4b6590dd7250 Uploaded miller-lab parents: diff changeset	204 nfrac = max([-1 * digits, 0])
4b6590dd7250 Uploaded miller-lab parents: diff changeset	205 vals = []
4b6590dd7250 Uploaded miller-lab parents: diff changeset	206
4b6590dd7250 Uploaded miller-lab parents: diff changeset	207 stop = graph_max
4b6590dd7250 Uploaded miller-lab parents: diff changeset	208 if loose:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	209 stop = graph_max + (0.5 * d)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	210
4b6590dd7250 Uploaded miller-lab parents: diff changeset	211 x = graph_min
4b6590dd7250 Uploaded miller-lab parents: diff changeset	212 while x <= stop:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	213 vals.append(int(x))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	214 x += d
4b6590dd7250 Uploaded miller-lab parents: diff changeset	215
4b6590dd7250 Uploaded miller-lab parents: diff changeset	216 vals = vals[1:]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	217
4b6590dd7250 Uploaded miller-lab parents: diff changeset	218 # if not loose:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	219 # if vals[-1] < graph_max:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	220 # vals.append(int(graph_max))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	221
4b6590dd7250 Uploaded miller-lab parents: diff changeset	222 labels = []
4b6590dd7250 Uploaded miller-lab parents: diff changeset	223 for val in vals:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	224 labels.append('{0}'.format(int(val/math.pow(10, digits))))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	225
4b6590dd7250 Uploaded miller-lab parents: diff changeset	226 # labels.append('{0:.1f}'.format(vals[-1]/math.pow(10, digits)))
4b6590dd7250 Uploaded miller-lab parents: diff changeset	227
4b6590dd7250 Uploaded miller-lab parents: diff changeset	228 return vals, labels
4b6590dd7250 Uploaded miller-lab parents: diff changeset	229
4b6590dd7250 Uploaded miller-lab parents: diff changeset	230 ################################################################################
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	231 ################################################################################
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	232 ################################################################################
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	233 ################################################################################
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	234
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	235 def space_for_legend(plot_params):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	236 space = 0.0
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	237
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	238 legend_states = plot_params['legend_states']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	239 if legend_states:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	240 ind_space = plot_params['ind_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	241 ind_height = plot_params['ind_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	242 space += len(legend_states) * (ind_space + ind_height) - ind_space
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	243
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	244 return space
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	245
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	246 ################################################################################
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	247
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	248 def space_for_chroms(plot_params, chroms, individuals, data):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	249 space_dict = {}
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	250
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	251 chrom_height = plot_params['chrom_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	252 ind_space = plot_params['ind_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	253 ind_height = plot_params['ind_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	254
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	255 for chrom in chroms:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	256 space_dict[chrom] = chrom_height
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	257
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	258 individual_count = 0
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	259 for individual in individuals:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	260 if individual in data[chrom]:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	261 individual_count += 1
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	262
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	263 space_dict[chrom] += individual_count * (ind_space + ind_height)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	264
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	265 return space_dict
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	266
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	267 ################################################################################
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	268
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	269 def make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir, state2name=None, populations=3):
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	270 fs_chrom_len = build_chrom_len_dict(input_dbkey, galaxy_data_index_dir)
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	271 chroms, individuals, data, chrom_len, used_states = parse_input_file(input_file)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	272
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	273 ## populate chrom_len
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	274 for chrom in chrom_len.keys():
4b6590dd7250 Uploaded miller-lab parents: diff changeset	275 if chrom in fs_chrom_len:
4b6590dd7250 Uploaded miller-lab parents: diff changeset	276 chrom_len[chrom] = fs_chrom_len[chrom]
4b6590dd7250 Uploaded miller-lab parents: diff changeset	277
4b6590dd7250 Uploaded miller-lab parents: diff changeset	278 #check_chroms(chroms, chrom_len, input_dbkey)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	279 check_data(data, chrom_len, input_dbkey)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	280
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	281 ## plot parameters
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	282 plot_params = {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	283 'plot_dpi': 300,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	284 'page_width': 8.50,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	285 'page_height': 11.00,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	286 'top_margin': 0.10,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	287 'bottom_margin': 0.10,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	288 'chrom_space': 0.25,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	289 'chrom_height': 0.25,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	290 'ind_space': 0.10,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	291 'ind_height': 0.25,
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	292 'legend_space': 0.10
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	293 }
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	294
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	295 ## in the legend, only print out states that are
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	296 ## 1) in the data
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	297 ## - AND -
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	298 ## 2) in the state2name map
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	299 legend_states = []
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	300 if state2name is not None:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	301 for state in used_states:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	302 if state in state2name:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	303 legend_states.append(state)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	304
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	305 plot_params['legend_states'] = legend_states
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	306
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	307 ## choose the correct make_state_rectangle method
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	308 if populations == 3:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	309 plot_params['rectangle_method'] = make_state_rectangle_3pop
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	310 elif populations == 2:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	311 plot_params['rectangle_method'] = make_state_rectangle_2pop
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	312
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	313 pdf_pages = PdfPages(output_file)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	314
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	315 ## generate a list of chroms for each page
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	316
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	317 needed_for_legend = space_for_legend(plot_params)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	318 needed_for_chroms = space_for_chroms(plot_params, chroms, individuals, data)
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	319
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	320 chrom_space_per_page = plot_params['page_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	321 chrom_space_per_page -= plot_params['top_margin'] + plot_params['bottom_margin']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	322 chrom_space_per_page -= needed_for_legend + plot_params['legend_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	323 chrom_space_per_page -= plot_params['chrom_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	324
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	325 chroms_left = chroms[:]
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	326 pages = []
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	327
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	328 space_left = chrom_space_per_page
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	329 chrom_list = []
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	330
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	331 while chroms_left:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	332 chrom = chroms_left.pop(0)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	333 space_needed = needed_for_chroms[chrom] + plot_params['chrom_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	334 if (space_needed > chrom_space_per_page):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	335 print >> sys.stderr, 'Multipage chroms not yet supported'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	336 sys.exit(1)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	337
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	338 ## sometimes 1.9 - 1.9 < 0 (-4.4408920985e-16)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	339 ## so, we make sure it's not more than a millimeter over
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	340 if space_left - space_needed > -0.04:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	341 chrom_list.append(chrom)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	342 space_left -= space_needed
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	343 else:
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	344 pages.append(chrom_list[:])
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	345 chrom_list = []
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	346 chroms_left.insert(0, chrom)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	347 space_left = chrom_space_per_page
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	348
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	349 ############################################################################
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	350
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	351 plot_dpi = plot_params['plot_dpi']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	352 page_width = plot_params['page_width']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	353 page_height = plot_params['page_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	354 top_margin = plot_params['top_margin']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	355 ind_space = plot_params['ind_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	356 ind_height = plot_params['ind_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	357 make_state_rectangle = plot_params['rectangle_method']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	358 legend_space = plot_params['legend_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	359 chrom_space = plot_params['chrom_space']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	360 chrom_height = plot_params['chrom_height']
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	361
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	362 for page in pages:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	363 fig = plt.figure(figsize=(page_width, page_height), dpi=plot_dpi)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	364 bottom = 1.0 - (top_margin/page_height)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	365
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	366 # print legend
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	367 if legend_states:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	368 top = True
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	369 for state in sorted(legend_states):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	370 if top:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	371 bottom -= ind_height/page_height
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	372 top = False
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	373 else:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	374 bottom -= (ind_space + ind_height)/page_height
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	375
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	376 ax1 = fig.add_axes([0.0, bottom, 0.09, ind_height/page_height])
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	377 plt.axis('off')
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	378 ax1.set_xlim(0, 1)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	379 ax1.set_ylim(0, 1)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	380 for patch in make_state_rectangle(0, 1, state, 'legend', state2name[state]):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	381 ax1.add_patch(patch)
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	382
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	383 ax2 = fig.add_axes([0.10, bottom, 0.88, ind_height/page_height], frame_on=False)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	384 plt.axis('off')
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	385 plt.text(0.0, 0.5, state2name[state], fontsize=10, ha='left', va='center')
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	386
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	387 bottom -= legend_space/page_height
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	388
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	389 # print chroms
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	390 top = True
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	391 for chrom in page:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	392 length = chrom_len[chrom]
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	393 vals, labels = tick_foo(0, length)
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	394
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	395 if top:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	396 bottom -= chrom_height/page_height
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	397 top = False
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	398 else:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	399 bottom -= (chrom_space + chrom_height)/page_height
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	400
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	401 ax = fig.add_axes([0.0, bottom, 1.0, chrom_height/page_height])
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	402 plt.axis('off')
4b6590dd7250 Uploaded miller-lab parents: diff changeset	403 plt.text(0.5, 0.5, chrom, fontsize=14, ha='center')
4b6590dd7250 Uploaded miller-lab parents: diff changeset	404
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	405 individual_count = 0
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	406 for individual in individuals:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	407 if individual in data[chrom]:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	408 individual_count += 1
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	409
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	410 i = 0
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	411 for individual in individuals:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	412 if individual in data[chrom]:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	413 i += 1
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	414 bottom -= (ind_space + ind_height)/page_height
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	415
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	416 ax1 = fig.add_axes([0.0, bottom, 0.09, ind_height/page_height])
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	417 plt.axis('off')
4b6590dd7250 Uploaded miller-lab parents: diff changeset	418 plt.text(1.0, 0.5, individual, fontsize=10, ha='right', va='center')
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	419
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	420 ax2 = fig.add_axes([0.10, bottom, 0.88, ind_height/page_height], frame_on=False)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	421 ax2.set_xlim(0, length)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	422 ax2.set_ylim(0, 1)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	423
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	424 if i != individual_count:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	425 plt.axis('off')
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	426 else:
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	427 ax2.tick_params(top=False, left=False, right=False, labelleft=False)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	428 ax2.set_xticks(vals)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	429 ax2.set_xticklabels(labels)
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	430
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	431 for p1, p2, state in sorted(data[chrom][individual]):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	432 for patch in make_state_rectangle(p1, p2, state, chrom, individual):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	433 ax2.add_patch(patch)
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	434
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	435 # extend last state to end of chrom
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	436 if p2 < length:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	437 for patch in make_state_rectangle(p2, length, state, chrom, individual):
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	438 ax2.add_patch(patch)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	439
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	440
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	441 pdf_pages.savefig(fig)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	442 plt.close(fig)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	443
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	444 pdf_pages.close()
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	445
4b6590dd7250 Uploaded miller-lab parents: diff changeset	446 ################################################################################
4b6590dd7250 Uploaded miller-lab parents: diff changeset	447
4b6590dd7250 Uploaded miller-lab parents: diff changeset	448 if __name__ == '__main__':
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	449 make_dpmix_plot('loxAfr3', 'output.dat', 'output2_files/picture.pdf', '/scratch/galaxy/home/oocyte/galaxy_oocyte/tool-data', state2name={0: 'heterochromatin', 1: 'reference', 2: 'asian'}, populations=2)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	450 # input_dbkey, input_file, output_file, galaxy_data_index_dir = sys.argv[1:5]
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	451 # make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir)
12 4b6590dd7250 Uploaded miller-lab parents: diff changeset	452 sys.exit(0)
4b6590dd7250 Uploaded miller-lab parents: diff changeset	453
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	454 ## notes
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	455 # 1) pass in a state to name mapping
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 12 diff changeset	456 # 2) only print out names for states which exist in the data, and are in the state to name mapping

Mercurial > repos > miller-lab > genome_diversity

annotate dpmix_plot.py @ 35:ea52b23f1141