Mercurial > repos > mzeidler > virana2

comparison vhom_regionplot.py @ 0:3ba5983012cf draft

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author mzeidler
date Tue, 24 Sep 2013 10:19:40 -0400
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children c5285cf678c1
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-1:000000000000 0:3ba5983012cf
1 import matplotlib.pyplot as plt
2
3 from matplotlib import rcParams
4 from matplotlib import colors
5 from matplotlib import cm
6
7 from argparse import ArgumentParser
8 from matplotlib.backends.backend_pdf import PdfPages
9
10 import os
11
12 import colorsys
13
14
15
16
17 rcParams['figure.figsize'] = (6, 6)
18 rcParams['figure.dpi'] = 100
19 rcParams['axes.facecolor'] = 'white'
20 rcParams['font.size'] = 10
21 rcParams['patch.edgecolor'] = 'white'
22 rcParams['patch.linewidth']=0.5
23 rcParams['patch.facecolor'] = 'black'
24 rcParams['font.family'] = 'StixGeneral'
25
26
27 def color_variants(r,g,b):
28 h,l2,s= colorsys.rgb_to_hls(r,g,b)
29 l=[l2-0.4,l2-0.1,l2+0.2]
30 hexs=[]
31 for i in l:
32 hexs.append(colors.rgb2hex(colorsys.hls_to_rgb(h,i,s)))
33 return hexs
34
35 def rgb_color_variants(r,g,b):
36 h,l2,s= colorsys.rgb_to_hls(r,g,b)
37 l=[l2-0.4,l2-0.1,l2+0.2]
38 rgbs={}
39 rgbs["pathogen"]=colorsys.hls_to_rgb(h,l[0],s)
40 rgbs["ambiguous"]=colorsys.hls_to_rgb(h,l[1],s)
41 rgbs["human"]=colorsys.hls_to_rgb(h,l[2],s)
42 return rgbs
43
44
45
46
47 def remove_border(axes=None, top=False, right=False, left=True, bottom=True):
48 """
49 Minimize chartjunk by stripping out unnecesasry plot borders and axis ticks
50
51 The top/right/left/bottom keywords toggle whether the corresponding plot border is drawn
52 """
53 ax = axes or plt.gca()
54 ax.spines['top'].set_visible(top)
55 ax.spines['right'].set_visible(right)
56 ax.spines['left'].set_visible(left)
57 ax.spines['bottom'].set_visible(bottom)
58
59 #turn off all ticks
60 ax.yaxis.set_ticks_position('none')
61 ax.xaxis.set_ticks_position('none')
62
63 #now re-enable visibles
64 if top:
65 ax.xaxis.tick_top()
66 if bottom:
67 ax.xaxis.tick_bottom()
68 if left:
69 ax.yaxis.tick_left()
70 if right:
71 ax.yaxis.tick_right()
72
73
74 def generateHTML(stat_dict,file,directory):
75 rval=["<html><head><title>Homologous groups and regions derived from hit files </title></head><body><p/>\n"]
76 rval.append("<a href='plot.pdf'>Download Plot</a>")
77 n_samples=0
78 for sample in stat_dict.iterkeys():
79 n_samples+=1
80 rval.append("<div id=%s_graph></div><p/>"%(sample))
81 rval.append("<script src='jquery-1.10.2.min.js'></script>")
82 rval.append("<script src='jqBarGraph.2.1.js'></script>")
83 rval.append('<script>')
84 i=0
85 for sample in stat_dict.iterkeys():
86 i+=1
87 rval.append("%s_array = new Array(" %sample)
88 for family in stat_dict[sample].iterkeys():
89 values=[]
90 for region,data in stat_dict[sample][family].iteritems():
91 values.append([int(data[0][1]),int(data[0][2]), data[0][0], data[0][3],int(data[0][4]),int(region)])
92 rval.append(str([values,family])+",")
93 rval[-1]=rval[-1][:-1]
94 rval.append(");")
95 rval.append("%s_files=%s;"%(sample,str(getFiles(directory))))
96 rval.append("$('#%s_graph').jqBarGraph({"%sample)
97 rval.append("sample: '%s',"%sample)
98 rval.append("data: %s_array,"%sample)
99 rval.append("files: %s_files,"%sample)
100 r,g,b,a=cm.hsv(1.*i/n_samples)
101 rval.append("colors: %s," %color_variants(r,g,b))
102 rval.append("legend: true,")
103 rval.append("tab: 'reads',")
104 rval.append("title: '<H3>Visualisation of Sample %s</H3>',"%sample)
105 rval.append("width: %d"%((len(stat_dict[sample])*50)+150))
106 rval.append("});")
107 # rval.append("jQuery.get('test.py', function(data) {")
108 # rval.append("alert(data)")
109 # rval.append("})")
110 rval.append("</script>")
111
112 rval.append( '</body></html>' )
113 with open(file,'w') as file:
114 file.write("\n".join( rval ))
115
116 def generatePyPlot(stat_dict,output_file):
117 pp = PdfPages(output_file)
118 fig = plt.figure()
119
120 n_samples=len(stat_dict)
121 dict={}
122 position={}
123 dict_label={}
124 for sample in stat_dict.iterkeys():
125 dict[sample]=[{},{}]
126 position[sample]={}
127 dict_label[sample]={}
128 j=0
129 for family in stat_dict[sample].iterkeys():
130
131 i=0
132 for region,values in stat_dict[sample][family].iteritems():
133
134 if i not in dict[sample][0]:
135 dict[sample][0][i]=[]
136 dict[sample][1][i]=[]
137 position[sample][i]=[]
138 dict_label[sample][i]=[]
139 dict[sample][0][i].append(int(values[0][1]))
140 dict[sample][1][i].append(int(values[0][2]))
141 position[sample][i].append(j)
142 dict_label[sample][i].append(values[0][0])
143 i+=1
144 j+=1
145
146 i=0
147 for sample in dict.iterkeys():
148 fig = plt.figure()
149 fig.subplots_adjust(bottom=0.25,hspace=0.5)
150 r,g,b,a=cm.hsv(1.*i/n_samples)
151 color_map=rgb_color_variants(r,g,b)
152 for sub in [0,1]:
153 plt.subplot(1,2,sub+1)
154 bottom={}
155 for level,values in dict[sample][sub].iteritems():
156 colors=[color_map[r] for r in dict_label[sample][level]]
157 if level==0:
158 print level, values, position[sample][level],bottom
159 plt.bar(position[sample][level],values,bottom=0, width=0.8 ,color=colors)
160 else:
161 lastvalues=[]
162 for oldpos in range(len(values)):
163 lastvalues.append(bottom[position[sample][level][oldpos]])
164 print level, values, position[sample][level], lastvalues
165 plt.bar(position[sample][level],values, width=0.8,bottom=lastvalues ,color=colors)
166 for pos in range(len(values)):
167 if position[sample][level][pos] not in bottom:
168 bottom[position[sample][level][pos]]=0
169 else:
170 bottom[position[sample][level][pos]]+=values[pos]
171 pos=[x+0.4 for x in range(len(stat_dict[sample]))]
172 plt.xticks(pos, stat_dict[sample].keys(), rotation='vertical')
173 if(sub==0):
174 plt.ylabel("Reads")
175 else:
176 plt.ylabel("Basepairs")
177 plt.xlabel("")
178 fig.subplots_adjust(bottom=0.25,wspace=0.5)
179 remove_border()
180 plt.suptitle(sample)
181 pp.savefig(fig)
182 i+=1
183 pp.close()
184
185
186
187 def parseStatFile(filename):
188
189 with open(filename,'r') as file:
190 values=[ map(str,line.split('\t')) for line in file ]
191
192 dict={}
193 for line in values[1:]:
194 if line[3] not in dict:
195 dict[line[3]]={}
196 dict[line[3]][line[1]]={}
197 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
198 else:
199 if line[1] not in dict[line[3]]:
200 dict[line[3]][line[1]]={}
201 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
202 else:
203 if line[2] not in dict[line[3]][line[1]]:
204 dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
205 else:
206 dict[line[3]][line[1]][line[2]].append([line[4],line[5],line[7],line[0],line[6]])
207 # for key in dict.iterkeys():
208 # for family_key,values in dict[key].iteritems():
209 # for line in values:
210 # print key,family_key,line
211 return dict
212 def getFiles(directory):
213 rval={}
214 dlist = os.listdir(directory)
215 for dire in dlist:
216 if(os.path.isdir(os.path.join(directory,dire))):
217 rval[dire]={}
218 flist = os.listdir(os.path.join(directory,dire))
219 for file in flist:
220 split=file.split("_")
221 region=split[1]
222 if region not in rval[dire]:
223 rval[dire][region]=[file]
224 else:
225 rval[dire][region].append(file)
226
227 return rval
228
229
230
231 if __name__ == "__main__":
232
233
234 parser = ArgumentParser()
235
236 a = parser.add_argument
237 a("--html_file",dest="html_file")
238 a("--directory",dest="directory")
239 a("--stats",dest="stat_file")
240
241 (options,args)= parser.parse_known_args()
242
243 # args.insert(0,"dummy")
244 # try:
245 # RegionRunner.run(argv=args)
246 # except SystemExit:
247
248 stat_dict=parseStatFile(options.stat_file)
249 generatePyPlot(stat_dict,os.path.join(options.directory,"plot.pdf"))
250 generateHTML(stat_dict,options.html_file,options.directory)
251
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