Mercurial > repos > mzeidler > virana_main

comparison vhom_regionplot.py @ 0:f63d639b223c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial Upload
author mzeidler
date Wed, 25 Sep 2013 11:41:16 -0400
parents
children ec82deba3cef
comparison
equal deleted inserted replaced
-1:000000000000 0:f63d639b223c
1 import matplotlib
2 matplotlib.use('Agg')
3 import matplotlib.pyplot as plt
4
5 from matplotlib import rcParams
6 from matplotlib import colors
7 from matplotlib import cm
8
9 from matplotlib.patches import Rectangle
10
11 from vhom import RegionRunner
12
13 from argparse import ArgumentParser
14 from matplotlib.backends.backend_pdf import PdfPages
15
16 import os
17 import shutil
18
19 import sys
20
21 import colorsys
22
23
24
25
26 rcParams['figure.figsize'] = (6, 6)
27 rcParams['figure.dpi'] = 100
28 rcParams['axes.facecolor'] = 'white'
29 rcParams['font.size'] = 10
30 rcParams['patch.edgecolor'] = 'white'
31 rcParams['patch.linewidth']=0.5
32 rcParams['patch.facecolor'] = 'black'
33 rcParams['font.family'] = 'StixGeneral'
34
35
36 def color_variants(r,g,b):
37 h,l2,s= colorsys.rgb_to_hls(r,g,b)
38 l=[l2-0.4,l2-0.1,l2+0.2]
39 hexs=[]
40 for i in l:
41 hexs.append(colors.rgb2hex(colorsys.hls_to_rgb(h,i,s)))
42 return hexs
43
44 def rgb_color_variants(r,g,b):
45 h,l2,s= colorsys.rgb_to_hls(r,g,b)
46 l=[l2-0.4,l2-0.1,l2+0.2]
47 rgbs={}
48 rgbs["pathogen"]=colorsys.hls_to_rgb(h,l[0],s)
49 rgbs["ambiguous"]=colorsys.hls_to_rgb(h,l[1],s)
50 rgbs["human"]=colorsys.hls_to_rgb(h,l[2],s)
51 return rgbs
52
53
54
55
56 def remove_border(axes=None, top=False, right=False, left=True, bottom=True):
57 """
58 Minimize chartjunk by stripping out unnecesasry plot borders and axis ticks
59
60 The top/right/left/bottom keywords toggle whether the corresponding plot border is drawn
61 """
62 ax = axes or plt.gca()
63 ax.spines['top'].set_visible(top)
64 ax.spines['right'].set_visible(right)
65 ax.spines['left'].set_visible(left)
66 ax.spines['bottom'].set_visible(bottom)
67
68 #turn off all ticks
69 ax.yaxis.set_ticks_position('none')
70 ax.xaxis.set_ticks_position('none')
71
72 #now re-enable visibles
73 if top:
74 ax.xaxis.tick_top()
75 if bottom:
76 ax.xaxis.tick_bottom()
77 if left:
78 ax.yaxis.tick_left()
79 if right:
80 ax.yaxis.tick_right()
81
82
83 def generateHTML(stat_dict,file,directory):
84 rval=["<html><head><title>Homologous groups and regions derived from hit files </title></head><body><p/>\n"]
85 rval.append("<a href='plot.pdf'>Download Plot</a>")
86 n_samples=0
87 for sample in stat_dict.iterkeys():
88 n_samples+=1
89 rval.append("<div id=%s_graph></div><p/>"%(sample))
90 curr_dir = os.path.dirname(os.path.realpath(__file__))
91 shutil.copy(os.path.join(curr_dir,"jquery-1.10.2.min.js"),directory)
92 shutil.copy(os.path.join(curr_dir,"jqBarGraph.2.1.min.js"),directory)
93 rval.append("<script type='text/javascript' src='jquery-1.10.2.min.js'></script>")
94 rval.append("<script type='text/javascript' src='jqBarGraph.2.1.min.js'></script>")
95 rval.append('<script>')
96 i=0
97 for sample in stat_dict.iterkeys():
98 i+=1
99 rval.append("%s_array = new Array(" %sample)
100 for family in stat_dict[sample].iterkeys():
101 values=[]
102 for region,data in stat_dict[sample][family].iteritems():
103 values.append([int(data[0][1]),int(data[0][2]), data[0][0], data[0][3],int(data[0][4]),int(region)])
104 rval.append(str([values,family])+",")
105 rval[-1]=rval[-1][:-1]
106 rval.append(");")
107 rval.append("%s_files=%s;"%(sample,str(getFiles(directory))))
108 rval.append("$('#%s_graph').jqBarGraph({"%sample)
109 rval.append("sample: '%s',"%sample)
110 rval.append("data: %s_array,"%sample)
111 rval.append("files: %s_files,"%sample)
112 r,g,b,a=cm.hsv(1.*i/n_samples)
113 rval.append("colors: %s," %color_variants(r,g,b))
114 rval.append("legend: true,")
115 rval.append("tab: 'reads',")
116 rval.append("title: '<H3>Visualisation of Sample %s</H3>',"%sample)
117 rval.append("width: %d"%((len(stat_dict[sample])*50)+150))
118 rval.append("});")
119 # rval.append("jQuery.get('test.py', function(data) {")
120 # rval.append("alert(data)")
121 # rval.append("})")
122 rval.append("</script>")
123
124 rval.append( '</body></html>' )
125 with open(file,'w') as file:
126 file.write("\n".join( rval ))
127 def transformDict(stat_dict):
128 dict={}
129 position={}
130 dict_label={}
131 for sample in stat_dict.iterkeys():
132 dict[sample]=[{},{}]
133 position[sample]={}
134 dict_label[sample]={}
135 j=0
136 for family in stat_dict[sample].iterkeys():
137
138 i=0
139 for region,values in stat_dict[sample][family].iteritems():
140
141 if i not in dict[sample][0]:
142 dict[sample][0][i]=[]
143 dict[sample][1][i]=[]
144 position[sample][i]=[]
145 dict_label[sample][i]=[]
146 dict[sample][0][i].append(int(values[0][1]))
147 dict[sample][1][i].append(int(values[0][2]))
148 position[sample][i].append(j)
149 dict_label[sample][i].append(values[0][0])
150 i+=1
151 j+=1
152 return dict,position,dict_label
153
154 def customeLegend(color_map):
155 legend_map=[[],[]]
156 for label in color_map:
157 box=Rectangle((0,0),1,1,color=color_map[label],fill=True)
158 legend_map[0].append(box)
159 legend_map[1].append(label)
160 plt.figlegend(legend_map[0],legend_map[1],loc=8,ncol=len(color_map))
161
162
163
164
165 def generatePyPlot(stat_dict,output_file):
166 pp = PdfPages(output_file)
167 fig = plt.figure()
168
169 n_samples=len(stat_dict)
170 dict,position,dict_label=transformDict(stat_dict)
171
172 i=0
173 for sample in dict.iterkeys():
174 fig = plt.figure()
175
176 fig.subplots_adjust(bottom=0.25,hspace=0.5)
177
178 r,g,b,a=cm.hsv(1.*i/n_samples)
179 color_map=rgb_color_variants(r,g,b)
180
181 for sub in [0,1]:
182 plt.subplot(1,2,sub+1)
183 bottom={}
184 for level,values in dict[sample][sub].iteritems():
185 colors=[color_map[r] for r in dict_label[sample][level]]
186
187 if level==0:
188
189 plt.bar(position[sample][level],values,bottom=0, width=0.8 ,color=colors)
190 else:
191 lastvalues=[]
192 for oldpos in range(len(values)):
193 lastvalues.append(bottom[position[sample][level][oldpos]])
194
195 plt.bar(position[sample][level],values, width=0.8,bottom=lastvalues ,color=colors)
196 for pos in range(len(values)):
197 if position[sample][level][pos] not in bottom:
198 bottom[position[sample][level][pos]]=0
199 else:
200 bottom[position[sample][level][pos]]+=values[pos]
201 pos=[x+0.4 for x in range(len(stat_dict[sample]))]
202 plt.xticks(pos, stat_dict[sample].keys(), rotation='vertical')
203 if(sub==0):
204 plt.ylabel("Cumulative reads assigned to family")
205 else:
206 plt.ylabel("Cumulative basepairs assigned to family")
207 plt.xlabel("")
208 fig.subplots_adjust(bottom=0.25,wspace=0.5)
209 remove_border()
210
211 customeLegend(color_map)
212 plt.suptitle(sample)
213 pp.savefig(fig)
214 i+=1
215 pp.close()
216
217
218
219 def parseStatFile(filename):
220
221 with open(filename,'r') as file:
222 values=[ map(str,line.split('\t')) for line in file ]
223
224 dict={}
225 for line in values[1:]:
226 if line[3] not in dict:
227 dict[line[3]]={}
228 dict[line[3]][line[1]]={}
229 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
230 else:
231 if line[1] not in dict[line[3]]:
232 dict[line[3]][line[1]]={}
233 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
234 else:
235 if line[2] not in dict[line[3]][line[1]]:
236 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
237 else:
238 dict[line[3]][line[1]][line[2]].append([line[4],line[5],line[7],line[0],line[6]])
239 # for key in dict.iterkeys():
240 # for family_key,values in dict[key].iteritems():
241 # for line in values:
242 # print key,family_key,line
243 return dict
244 def getFiles(directory):
245 rval={}
246 dlist = os.listdir(directory)
247 for dire in dlist:
248 if(os.path.isdir(os.path.join(directory,dire))):
249 rval[dire]={}
250 flist = os.listdir(os.path.join(directory,dire))
251 for file in flist:
252 split=file.split("_")
253 region=split[1]
254 if region not in rval[dire]:
255 rval[dire][region]=[file]
256 else:
257 rval[dire][region].append(file)
258
259 return rval
260
261
262
263 if __name__ == "__main__":
264
265
266 parser = ArgumentParser()
267
268 a = parser.add_argument
269 a("--html_file",dest="html_file")
270 a("--directory",dest="directory")
271 a("--stats",dest="stat_file")
272
273 (options,args)= parser.parse_known_args()
274
275 args.insert(0,"dummy")
276 try:
277 RegionRunner.run(argv=args)
278 except SystemExit:
279 stat_dict=parseStatFile(options.stat_file)
280 generatePyPlot(stat_dict,os.path.join(options.directory,"plot.pdf"))
281 generateHTML(stat_dict,options.html_file,options.directory)
282
283
284
285
286