Mercurial > repos > miller-lab > genome_diversity
annotate dpmix_plot.py @ 28:184d14e4270d
Update to Miller Lab devshed revision 4ede22dd5500
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 17 Jul 2013 12:46:46 -0400 |
| parents | 8997f2ca8c7a |
| children | a631c2f6d913 |
| rev | line source |
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| 12 | 1 #!/usr/bin/env python |
| 2 | |
| 3 import os | |
| 4 import sys | |
| 5 import math | |
| 6 import matplotlib as mpl | |
| 7 mpl.use('PDF') | |
| 8 import matplotlib.pyplot as plt | |
| 9 from matplotlib.path import Path | |
| 10 import matplotlib.patches as patches | |
| 11 | |
| 12 ################################################################################ | |
| 13 | |
| 14 def build_chrom_len_dict(dbkey, galaxy_data_index_dir): | |
| 15 chrom_len_root = os.path.join(galaxy_data_index_dir, 'shared/ucsc/chrom') | |
| 16 chrom_len_file = '{0}.len'.format(dbkey) | |
| 17 chrom_len_path = os.path.join(chrom_len_root, chrom_len_file) | |
| 18 | |
| 19 chrom_len = {} | |
| 20 | |
| 21 try: | |
| 22 with open(chrom_len_path) as fh: | |
| 23 for line in fh: | |
| 24 line = line.rstrip('\r\n') | |
| 25 elems = line.split() | |
| 26 if len(elems) == 2: | |
| 27 chrom = elems[0] | |
| 28 length = int(elems[1]) | |
| 29 chrom_len[chrom] = length | |
| 30 except: | |
| 31 pass | |
| 32 | |
| 33 return chrom_len | |
| 34 | |
| 35 def parse_input_file(input_file): | |
| 36 chroms = [] | |
| 37 individuals = [] | |
| 38 data = {} | |
| 39 chrom_len = {} | |
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40 used_states = [] |
| 12 | 41 |
| 42 with open(input_file) as fh: | |
| 43 for line in fh: | |
| 44 line = line.strip() | |
| 45 if line: | |
| 46 elems = line.split() | |
| 47 chrom = elems[0] | |
| 48 p1, p2, state = map(int, elems[1:4]) | |
| 49 id = elems[4] | |
| 50 | |
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51 if state not in used_states: |
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52 used_states.append(state) |
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53 |
| 12 | 54 if chrom not in chroms: |
| 55 chroms.append(chrom) | |
| 56 | |
| 57 if id not in individuals: | |
| 58 individuals.append(id) | |
| 59 | |
| 60 data.setdefault(chrom, {}) | |
| 61 data[chrom].setdefault(id, []) | |
| 62 data[chrom][id].append((p1, p2, state)) | |
| 63 | |
| 64 if p2 > chrom_len.setdefault(chrom, 0): | |
| 65 chrom_len[chrom] = p2 | |
| 66 | |
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67 return chroms, individuals, data, chrom_len, used_states |
| 12 | 68 |
| 69 def check_chroms(chroms, chrom_len, dbkey): | |
| 70 error = 0 | |
| 71 for chrom in chroms: | |
| 72 if chrom not in chrom_len: | |
| 73 print >> sys.stderr, "Can't find length for {0} chromosome {1}".format(dbkey, chrom) | |
| 74 error = 1 | |
| 75 if error: | |
| 76 sys.exit(1) | |
| 77 | |
| 78 def check_data(data, chrom_len, dbkey): | |
| 79 error = 0 | |
| 80 for chrom in data: | |
| 81 chrom_beg = 0 | |
| 82 chrom_end = chrom_len[chrom] | |
| 83 for individual in data[chrom]: | |
| 84 for p1, p2, state in data[chrom][individual]: | |
| 85 if p1 >= p2: | |
| 86 print >> sys.stderr, "Bad data line: begin >= end: {0} {1} {2} {3}".format(chrom, p1, p2, state, individual) | |
| 87 error = 1 | |
| 88 if p1 < chrom_beg or p2 > chrom_end: | |
| 89 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) | |
| 90 error = 1 | |
| 91 if error: | |
| 92 sys.exit(1) | |
| 93 | |
| 94 def make_rectangle(p1, p2, color, bottom=0.0, top=1.0): | |
| 95 verts = [ | |
| 96 (p1, bottom), # left, bottom | |
| 97 (p1, top), # left, top | |
| 98 (p2, top), # right, top | |
| 99 (p2, bottom), # right, bottom | |
| 100 (0.0, 0.0) # ignored | |
| 101 ] | |
| 102 | |
| 103 codes = [ | |
| 104 Path.MOVETO, | |
| 105 Path.LINETO, | |
| 106 Path.LINETO, | |
| 107 Path.LINETO, | |
| 108 Path.CLOSEPOLY | |
| 109 ] | |
| 110 | |
| 111 path = Path(verts, codes) | |
| 112 return patches.PathPatch(path, facecolor=color, lw=0) | |
| 113 | |
| 114 def make_split_rectangle(p1, p2, top_color, bottom_color): | |
| 115 patch1 = make_rectangle(p1, p2, bottom_color, top=0.5) | |
| 116 patch2 = make_rectangle(p1, p2, top_color, bottom=0.5) | |
| 117 return [patch1, patch2] | |
| 118 | |
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119 def make_state_rectangle_2pop(p1, p2, state, chrom, individual): |
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120 p1_color = 'r' |
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121 p2_color = 'g' |
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122 heterochromatin_color = '#c7c7c7' |
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123 |
| 12 | 124 if state == 0: |
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125 return [ make_rectangle(p1, p2, heterochromatin_color) ] |
| 12 | 126 elif state == 1: |
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127 return [ make_rectangle(p1, p2, p1_color) ] |
| 12 | 128 elif state == 2: |
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129 return [ make_rectangle(p1, p2, p2_color) ] |
| 12 | 130 elif state == 3: |
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131 return make_split_rectangle(p1, p2, p1_color, p2_color) |
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132 else: |
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133 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual) |
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134 sys.exit(1) |
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135 |
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136 def make_state_rectangle_3pop(p1, p2, state, chrom, individual): |
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137 p1_color = 'r' |
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138 p2_color = 'g' |
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139 p3_color = 'b' |
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140 heterochromatin_color = '#c7c7c7' |
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141 |
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142 if state == 0: |
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143 return [ make_rectangle(p1, p2, heterochromatin_color) ] |
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144 if state == 1: |
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145 return [ make_rectangle(p1, p2, p1_color) ] |
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146 if state == 2: |
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147 return [ make_rectangle(p1, p2, p2_color) ] |
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148 if state == 3: |
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149 return [ make_rectangle(p1, p2, p3_color) ] |
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150 if state == 4: |
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151 return make_split_rectangle(p1, p2, p1_color, p2_color) |
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152 if state == 5: |
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153 return make_split_rectangle(p1, p2, p1_color, p3_color) |
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154 if state == 6: |
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155 return make_split_rectangle(p1, p2, p2_color, p3_color) |
| 12 | 156 else: |
| 157 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual) | |
| 158 sys.exit(1) | |
| 159 | |
| 160 def nicenum(num, round=False): | |
| 161 if num == 0: | |
| 162 return 0.0 | |
| 163 | |
| 164 exp = int(math.floor(math.log10(num))) | |
| 165 f = num / math.pow(10, exp) | |
| 166 | |
| 167 if round: | |
| 168 if f < 1.5: | |
| 169 nf = 1.0 | |
| 170 elif f < 3.0: | |
| 171 nf = 2.0 | |
| 172 elif f < 7.0: | |
| 173 nf = 5.0 | |
| 174 else: | |
| 175 nf = 10.0 | |
| 176 else: | |
| 177 if f <= 1.0: | |
| 178 nf = 1.0 | |
| 179 elif f <= 2.0: | |
| 180 nf = 2.0 | |
| 181 elif f <= 5.0: | |
| 182 nf = 5.0 | |
| 183 else: | |
| 184 nf = 10.0 | |
| 185 | |
| 186 return nf * pow(10, exp) | |
| 187 | |
| 188 def tick_foo(beg, end, loose=False): | |
| 189 ntick = 10 | |
| 190 | |
| 191 range = nicenum(end - beg, round=False) | |
| 192 d = nicenum(range/(ntick - 1), round=True) | |
| 193 digits = int(math.floor(math.log10(d))) | |
| 194 | |
| 195 if loose: | |
| 196 graph_min = math.floor(beg/d) * d | |
| 197 graph_max = math.ceil(end/d) * d | |
| 198 else: | |
| 199 graph_min = beg | |
| 200 graph_max = end | |
| 201 | |
| 202 nfrac = max([-1 * digits, 0]) | |
| 203 vals = [] | |
| 204 | |
| 205 stop = graph_max | |
| 206 if loose: | |
| 207 stop = graph_max + (0.5 * d) | |
| 208 | |
| 209 x = graph_min | |
| 210 while x <= stop: | |
| 211 vals.append(int(x)) | |
| 212 x += d | |
| 213 | |
| 214 vals = vals[1:] | |
| 215 | |
| 216 # if not loose: | |
| 217 # if vals[-1] < graph_max: | |
| 218 # vals.append(int(graph_max)) | |
| 219 | |
| 220 labels = [] | |
| 221 for val in vals: | |
| 222 labels.append('{0}'.format(int(val/math.pow(10, digits)))) | |
| 223 | |
| 224 # labels.append('{0:.1f}'.format(vals[-1]/math.pow(10, digits))) | |
| 225 | |
| 226 return vals, labels | |
| 227 | |
| 228 ################################################################################ | |
| 229 | |
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230 def make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir, state2name=None, populations=3): |
| 12 | 231 fs_chrom_len = build_chrom_len_dict(input_dbkey, galaxy_data_index_dir) |
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232 chroms, individuals, data, chrom_len, used_states = parse_input_file(input_file) |
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233 |
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234 if populations == 3: |
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235 make_state_rectangle = make_state_rectangle_3pop |
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236 elif populations == 2: |
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237 make_state_rectangle = make_state_rectangle_2pop |
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238 else: |
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239 pass |
| 12 | 240 |
| 241 for chrom in chrom_len.keys(): | |
| 242 if chrom in fs_chrom_len: | |
| 243 chrom_len[chrom] = fs_chrom_len[chrom] | |
| 244 | |
| 245 #check_chroms(chroms, chrom_len, input_dbkey) | |
| 246 check_data(data, chrom_len, input_dbkey) | |
| 247 | |
| 248 ## units below are inches | |
| 249 top_space = 0.10 | |
| 250 chrom_space = 0.25 | |
| 251 chrom_height = 0.25 | |
| 252 ind_space = 0.10 | |
| 253 ind_height = 0.25 | |
| 254 | |
| 255 total_height = 0.0 | |
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256 |
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257 ## make a legend |
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258 ## only print out states that are |
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259 ## 1) in the data |
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260 ## - AND - |
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261 ## 2) in the state2name map |
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262 ## here, we only calculate the space needed |
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263 legend_states = [] |
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264 if state2name is not None: |
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265 for state in used_states: |
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266 if state in state2name: |
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267 legend_states.append(state) |
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268 |
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269 if legend_states: |
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270 total_height += len(legend_states) * (ind_space + ind_height) |
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271 total_height += (top_space - ind_space) |
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272 at_top = False |
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273 else: |
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274 at_top = True |
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275 |
| 12 | 276 for chrom in chroms: |
| 277 if at_top: | |
| 278 total_height += (top_space + chrom_height) | |
| 279 at_top = False | |
| 280 else: | |
| 281 total_height += (top_space + chrom_space + chrom_height) | |
| 282 | |
| 283 individual_count = 0 | |
| 284 for individual in individuals: | |
| 285 if individual in data[chrom]: | |
| 286 individual_count += 1 | |
| 287 total_height += individual_count * (ind_space + ind_height) | |
| 288 | |
| 289 width = 7.5 | |
| 290 height = math.ceil(total_height) | |
| 291 | |
| 292 bottom = 1.0 | |
| 293 | |
| 294 fig = plt.figure(figsize=(width, height)) | |
| 295 | |
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296 if legend_states: |
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297 at_top = True |
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298 for state in sorted(legend_states): |
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299 if at_top: |
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300 bottom -= (top_space + ind_height)/height |
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301 at_top = False |
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302 else: |
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303 bottom -= (ind_space + ind_height)/height |
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304 ## add code here to draw legend |
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305 # [left, bottom, width, height] |
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306 ax1 = fig.add_axes([0.0, bottom, 0.09, ind_height/height]) |
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307 plt.axis('off') |
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308 ax1.set_xlim(0, 1) |
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309 ax1.set_ylim(0, 1) |
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310 for patch in make_state_rectangle(0, 1, state, 'legend', state2name[state]): |
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311 ax1.add_patch(patch) |
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312 |
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313 ax2 = fig.add_axes([0.10, bottom, 0.88, ind_height/height], frame_on=False) |
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314 plt.axis('off') |
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315 plt.text(0.0, 0.5, state2name[state], fontsize=10, ha='left', va='center') |
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316 else: |
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317 at_top = True |
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318 |
| 12 | 319 for_webb = False |
| 320 | |
| 321 for chrom in chroms: | |
| 322 length = chrom_len[chrom] | |
| 323 vals, labels = tick_foo(0, length) | |
| 324 | |
| 325 if at_top: | |
| 326 bottom -= (top_space + chrom_height)/height | |
| 327 at_top = False | |
| 328 else: | |
| 329 bottom -= (top_space + chrom_space + chrom_height)/height | |
| 330 | |
| 331 if not for_webb: | |
| 332 ax = fig.add_axes([0.0, bottom, 1.0, chrom_height/height]) | |
| 333 plt.axis('off') | |
| 334 plt.text(0.5, 0.5, chrom, fontsize=14, ha='center') | |
| 335 | |
| 336 individual_count = 0 | |
| 337 for individual in individuals: | |
| 338 if individual in data[chrom]: | |
| 339 individual_count += 1 | |
| 340 | |
| 341 i = 0 | |
| 342 for individual in individuals: | |
| 343 if individual in data[chrom]: | |
| 344 i += 1 | |
| 345 | |
| 346 bottom -= (ind_space + ind_height)/height | |
| 347 if not for_webb: | |
| 348 # [left, bottom, width, height] | |
| 349 ax1 = fig.add_axes([0.0, bottom, 0.09, ind_height/height]) | |
| 350 plt.axis('off') | |
| 351 plt.text(1.0, 0.5, individual, fontsize=10, ha='right', va='center') | |
| 352 # [left, bottom, width, height] | |
| 353 ax2 = fig.add_axes([0.10, bottom, 0.88, ind_height/height], frame_on=False) | |
| 354 ax2.set_xlim(0, length) | |
| 355 ax2.set_ylim(0, 1) | |
| 356 if i != individual_count: | |
| 357 plt.axis('off') | |
| 358 else: | |
| 359 if not for_webb: | |
| 360 ax2.tick_params(top=False, left=False, right=False, labelleft=False) | |
| 361 ax2.set_xticks(vals) | |
| 362 ax2.set_xticklabels(labels) | |
| 363 else: | |
| 364 plt.axis('off') | |
| 365 for p1, p2, state in sorted(data[chrom][individual]): | |
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366 #for patch in make_state_rectangle(p1, p2, state, chrom, individual): |
| 12 | 367 for patch in make_state_rectangle(p1, p2, state, chrom, individual): |
| 368 ax2.add_patch(patch) | |
| 369 | |
| 370 plt.savefig(output_file) | |
| 371 | |
| 372 ################################################################################ | |
| 373 | |
| 374 if __name__ == '__main__': | |
| 375 input_dbkey, input_file, output_file, galaxy_data_index_dir = sys.argv[1:5] | |
| 376 make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir) | |
| 377 sys.exit(0) | |
| 378 | |
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379 ## notes |
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380 # 1) pass in a state to name mapping |
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381 # 2) only print out names for states which exist in the data, and are in the state to name mapping |