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
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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 import math
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6
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7 import matplotlib as mpl
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8 mpl.use('PDF')
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9 from matplotlib.backends.backend_pdf import PdfPages
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10 import matplotlib.pyplot as plt
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11 from matplotlib.path import Path
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12 import matplotlib.patches as patches
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14 ################################################################################
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15
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16 def build_chrom_len_dict(dbkey, galaxy_data_index_dir):
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17 chrom_len_root = os.path.join(galaxy_data_index_dir, 'shared/ucsc/chrom')
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18 chrom_len_file = '{0}.len'.format(dbkey)
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19 chrom_len_path = os.path.join(chrom_len_root, chrom_len_file)
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20
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21 chrom_len = {}
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22
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23 try:
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24 with open(chrom_len_path) as fh:
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25 for line in fh:
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26 line = line.rstrip('\r\n')
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27 elems = line.split()
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28 if len(elems) == 2:
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29 chrom = elems[0]
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30 length = int(elems[1])
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31 chrom_len[chrom] = length
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32 except:
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33 pass
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34
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35 return chrom_len
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36
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37 def parse_input_file(input_file):
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38 chroms = []
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39 individuals = []
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40 data = {}
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41 chrom_len = {}
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42 used_states = []
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43
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44 with open(input_file) as fh:
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45 for line in fh:
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46 line = line.strip()
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47 if line:
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48 elems = line.split()
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49 chrom = elems[0]
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50 p1, p2, state = map(int, elems[1:4])
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51 id = elems[4]
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52
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53 if state not in used_states:
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54 used_states.append(state)
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55
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56 if chrom not in chroms:
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57 chroms.append(chrom)
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58
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59 if id not in individuals:
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60 individuals.append(id)
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61
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62 data.setdefault(chrom, {})
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63 data[chrom].setdefault(id, [])
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64 data[chrom][id].append((p1, p2, state))
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65
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66 if p2 > chrom_len.setdefault(chrom, 0):
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67 chrom_len[chrom] = p2
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68
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69 return chroms, individuals, data, chrom_len, used_states
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70
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71 def check_chroms(chroms, chrom_len, dbkey):
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72 error = 0
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73 for chrom in chroms:
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74 if chrom not in chrom_len:
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75 print >> sys.stderr, "Can't find length for {0} chromosome {1}".format(dbkey, chrom)
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76 error = 1
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77 if error:
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78 sys.exit(1)
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79
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80 def check_data(data, chrom_len, dbkey):
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81 error = 0
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82 for chrom in data:
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83 chrom_beg = 0
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84 chrom_end = chrom_len[chrom]
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85 for individual in data[chrom]:
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86 for p1, p2, state in data[chrom][individual]:
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87 if p1 >= p2:
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88 print >> sys.stderr, "Bad data line: begin >= end: {0} {1} {2} {3}".format(chrom, p1, p2, state, individual)
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89 error = 1
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90 if p1 < chrom_beg or p2 > chrom_end:
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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)
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92 error = 1
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93 if error:
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94 sys.exit(1)
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95
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96 def make_rectangle(p1, p2, color, bottom=0.0, top=1.0):
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97 verts = [
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98 (p1, bottom), # left, bottom
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99 (p1, top), # left, top
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100 (p2, top), # right, top
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101 (p2, bottom), # right, bottom
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102 (0.0, 0.0) # ignored
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103 ]
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104
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105 codes = [
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106 Path.MOVETO,
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107 Path.LINETO,
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108 Path.LINETO,
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109 Path.LINETO,
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110 Path.CLOSEPOLY
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111 ]
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112
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113 path = Path(verts, codes)
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114 return patches.PathPatch(path, facecolor=color, lw=0)
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115
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116 def make_split_rectangle(p1, p2, top_color, bottom_color):
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117 patch1 = make_rectangle(p1, p2, bottom_color, top=0.5)
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118 patch2 = make_rectangle(p1, p2, top_color, bottom=0.5)
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119 return [patch1, patch2]
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120
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121 def make_state_rectangle_2pop(p1, p2, state, chrom, individual):
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122 p1_color = 'r'
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123 p2_color = 'g'
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124 heterochromatin_color = '#c7c7c7'
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125
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126 if state == 0:
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127 return [ make_rectangle(p1, p2, heterochromatin_color) ]
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128 elif state == 1:
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129 return [ make_rectangle(p1, p2, p1_color) ]
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130 elif state == 2:
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131 return [ make_rectangle(p1, p2, p2_color) ]
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132 elif state == 3:
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133 return make_split_rectangle(p1, p2, p1_color, p2_color)
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134 else:
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135 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual)
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136 sys.exit(1)
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137
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138 def make_state_rectangle_3pop(p1, p2, state, chrom, individual):
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139 p1_color = 'r'
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140 p2_color = 'g'
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141 p3_color = 'b'
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142 heterochromatin_color = '#c7c7c7'
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143
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144 if state == 0:
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145 return [ make_rectangle(p1, p2, heterochromatin_color) ]
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146 if state == 1:
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147 return [ make_rectangle(p1, p2, p1_color) ]
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148 if state == 2:
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149 return [ make_rectangle(p1, p2, p2_color) ]
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150 if state == 3:
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151 return [ make_rectangle(p1, p2, p3_color) ]
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152 if state == 4:
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153 return make_split_rectangle(p1, p2, p1_color, p2_color)
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154 if state == 5:
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155 return make_split_rectangle(p1, p2, p1_color, p3_color)
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156 if state == 6:
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157 return make_split_rectangle(p1, p2, p2_color, p3_color)
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158 else:
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159 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual)
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160 sys.exit(1)
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161
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162 def nicenum(num, round=False):
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163 if num == 0:
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164 return 0.0
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165
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166 exp = int(math.floor(math.log10(num)))
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167 f = num / math.pow(10, exp)
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168
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169 if round:
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170 if f < 1.5:
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171 nf = 1.0
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172 elif f < 3.0:
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173 nf = 2.0
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174 elif f < 7.0:
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175 nf = 5.0
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176 else:
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177 nf = 10.0
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178 else:
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179 if f <= 1.0:
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180 nf = 1.0
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181 elif f <= 2.0:
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182 nf = 2.0
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183 elif f <= 5.0:
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184 nf = 5.0
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185 else:
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186 nf = 10.0
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187
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188 return nf * pow(10, exp)
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189
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190 def tick_foo(beg, end, loose=False):
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191 ntick = 10
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192
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193 range = nicenum(end - beg, round=False)
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194 d = nicenum(range/(ntick - 1), round=True)
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195 digits = int(math.floor(math.log10(d)))
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196
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197 if loose:
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198 graph_min = math.floor(beg/d) * d
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199 graph_max = math.ceil(end/d) * d
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200 else:
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201 graph_min = beg
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202 graph_max = end
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203
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204 nfrac = max([-1 * digits, 0])
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205 vals = []
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206
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207 stop = graph_max
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208 if loose:
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209 stop = graph_max + (0.5 * d)
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210
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211 x = graph_min
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212 while x <= stop:
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213 vals.append(int(x))
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214 x += d
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215
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216 vals = vals[1:]
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217
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218 # if not loose:
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219 # if vals[-1] < graph_max:
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220 # vals.append(int(graph_max))
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221
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222 labels = []
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223 for val in vals:
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224 labels.append('{0}'.format(int(val/math.pow(10, digits))))
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225
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226 # labels.append('{0:.1f}'.format(vals[-1]/math.pow(10, digits)))
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227
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228 return vals, labels
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229
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230 ################################################################################
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231 ################################################################################
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232 ################################################################################
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233 ################################################################################
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234
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235 def space_for_legend(plot_params):
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236 space = 0.0
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237
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238 legend_states = plot_params['legend_states']
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239 if legend_states:
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240 ind_space = plot_params['ind_space']
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241 ind_height = plot_params['ind_height']
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242 space += len(legend_states) * (ind_space + ind_height) - ind_space
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243
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244 return space
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245
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246 ################################################################################
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247
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248 def space_for_chroms(plot_params, chroms, individuals, data):
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249 space_dict = {}
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250
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251 chrom_height = plot_params['chrom_height']
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252 ind_space = plot_params['ind_space']
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253 ind_height = plot_params['ind_height']
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254
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255 for chrom in chroms:
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256 space_dict[chrom] = chrom_height
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257
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258 individual_count = 0
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259 for individual in individuals:
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260 if individual in data[chrom]:
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261 individual_count += 1
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262
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263 space_dict[chrom] += individual_count * (ind_space + ind_height)
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264
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265 return space_dict
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266
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267 ################################################################################
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268
27
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269 def make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir, state2name=None, populations=3):
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270 fs_chrom_len = build_chrom_len_dict(input_dbkey, galaxy_data_index_dir)
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271 chroms, individuals, data, chrom_len, used_states = parse_input_file(input_file)
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272
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273 ## populate chrom_len
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274 for chrom in chrom_len.keys():
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275 if chrom in fs_chrom_len:
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276 chrom_len[chrom] = fs_chrom_len[chrom]
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277
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278 #check_chroms(chroms, chrom_len, input_dbkey)
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279 check_data(data, chrom_len, input_dbkey)
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280
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281 ## plot parameters
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282 plot_params = {
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283 'plot_dpi': 300,
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284 'page_width': 8.50,
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285 'page_height': 11.00,
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286 'top_margin': 0.10,
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287 'bottom_margin': 0.10,
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288 'chrom_space': 0.25,
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289 'chrom_height': 0.25,
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290 'ind_space': 0.10,
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291 'ind_height': 0.25,
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292 'legend_space': 0.10
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293 }
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294
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295 ## in the legend, only print out states that are
27
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296 ## 1) in the data
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297 ## - AND -
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298 ## 2) in the state2name map
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299 legend_states = []
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300 if state2name is not None:
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301 for state in used_states:
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302 if state in state2name:
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303 legend_states.append(state)
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diff changeset
304
31
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diff changeset
305 plot_params['legend_states'] = legend_states
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306
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307 ## choose the correct make_state_rectangle method
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308 if populations == 3:
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diff changeset
309 plot_params['rectangle_method'] = make_state_rectangle_3pop
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diff changeset
310 elif populations == 2:
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diff changeset
311 plot_params['rectangle_method'] = make_state_rectangle_2pop
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diff changeset
312
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diff changeset
313 pdf_pages = PdfPages(output_file)
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314
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315 ## generate a list of chroms for each page
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diff changeset
316
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diff changeset
317 needed_for_legend = space_for_legend(plot_params)
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diff changeset
318 needed_for_chroms = space_for_chroms(plot_params, chroms, individuals, data)
27
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diff changeset
319
31
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diff changeset
320 chrom_space_per_page = plot_params['page_height']
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diff changeset
321 chrom_space_per_page -= plot_params['top_margin'] + plot_params['bottom_margin']
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diff changeset
322 chrom_space_per_page -= needed_for_legend + plot_params['legend_space']
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diff changeset
323 chrom_space_per_page -= plot_params['chrom_space']
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diff changeset
324
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diff changeset
325 chroms_left = chroms[:]
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diff changeset
326 pages = []
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parents: 27
diff changeset
327
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diff changeset
328 space_left = chrom_space_per_page
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
329 chrom_list = []
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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)
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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
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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[:])
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
345 chrom_list = []
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
346 chroms_left.insert(0, chrom)
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
347 space_left = chrom_space_per_page
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348
31
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
349 ############################################################################
12
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diff changeset
350
31
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
351 plot_dpi = plot_params['plot_dpi']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
352 page_width = plot_params['page_width']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
353 page_height = plot_params['page_height']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
354 top_margin = plot_params['top_margin']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
355 ind_space = plot_params['ind_space']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
356 ind_height = plot_params['ind_height']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
357 make_state_rectangle = plot_params['rectangle_method']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
358 legend_space = plot_params['legend_space']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
359 chrom_space = plot_params['chrom_space']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
360 chrom_height = plot_params['chrom_height']
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
361
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
362 for page in pages:
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
363 fig = plt.figure(figsize=(page_width, page_height), dpi=plot_dpi)
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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
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
367 if legend_states:
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
368 top = True
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
369 for state in sorted(legend_states):
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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
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
372 top = False
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
373 else:
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
374 bottom -= (ind_space + ind_height)/page_height
27
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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)
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
379 ax1.set_ylim(0, 1)
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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)
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Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
384 plt.axis('off')
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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')
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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
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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
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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)
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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
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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
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402 plt.axis('off')
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403 plt.text(0.5, 0.5, chrom, fontsize=14, ha='center')
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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
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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
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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])
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417 plt.axis('off')
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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
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diff changeset
427 ax2.tick_params(top=False, left=False, right=False, labelleft=False)
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parents:
diff changeset
428 ax2.set_xticks(vals)
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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
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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
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diff changeset
445
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parents:
diff changeset
446 ################################################################################
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diff changeset
447
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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
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diff changeset
452 sys.exit(0)
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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