Mercurial > repos > glogobyte > viztool

comparison viz_graphs.py @ 17:a09d238416ba draft

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author glogobyte
date Wed, 28 Oct 2020 07:42:50 +0000
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16:34ffe50a8da6 17:a09d238416ba
1 import sys
2
3 # Read a file and return it as a list
4 def read(path, flag):
5 if flag == 0:
6 with open(path) as fp:
7 file=fp.readlines()
8 fp.close()
9 return file
10
11 if flag == 1:
12 with open(path) as fp:
13 file = fp.read().splitlines()
14 fp.close()
15 return file
16
17
18 #################################################################################################
19 def pdf_before_DE(analysis):
20
21 # Import FPDF class
22 from fpdf import FPDF, fpdf
23
24 # Import glob module to find all the files matching a pattern
25 import glob
26
27 # Image extensions
28 if analysis=="2":
29 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_non.png","spider_red.png","spider_non_red.png","c_logo.png","t_logo.png","c_bar.png","t_bar.png")
30 else:
31 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png")
32 # This list will hold the images file names
33 images = []
34
35 # Build the image list by merging the glob results (a list of files)
36 # for each extension. We are taking images from current folder.
37 for extension in image_extensions:
38 images.extend(glob.glob(extension))
39 #sys.exit(images)
40 # Create instance of FPDF class
41 pdf = FPDF('P', 'in', 'A4')
42 # Add new page. Without this you cannot create the document.
43 pdf.add_page()
44 # Set font to Arial, 'B'old, 16 pts
45 pdf.set_font('Arial', 'B', 20.0)
46
47 # Page header
48 pdf.cell(pdf.w-0.5, 0.5, 'IsomiR Profile Report',align='C')
49 pdf.ln(0.7)
50 pdf.set_font('Arial','', 16.0)
51 pdf.cell(pdf.w-0.5, 0.5, 'sRNA Length Distribution',align='C')
52
53 # Smaller font for image captions
54 pdf.set_font('Arial', '', 11.0)
55
56 # Image caption
57 pdf.ln(0.5)
58
59 yh=FPDF.get_y(pdf)
60 pdf.image(images[0],x=0.3,w=4, h=3)
61 pdf.image(images[1],x=4,y=yh, w=4, h=3)
62 pdf.ln(0.3)
63
64 # Image caption
65 pdf.cell(0.2)
66 pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precussor arm reference DB (5p and 3p arms) in Control (left)")
67 pdf.ln(0.2)
68 pdf.cell(0.2)
69 pdf.cell(3.0, 0.0, " and Treated (right) groups")
70
71
72 pdf.ln(0.5)
73 h1=FPDF.get_y(pdf)
74 pdf.image(images[2],x=1, w=6.5, h=5)
75 h2=FPDF.get_y(pdf)
76 FPDF.set_y(pdf,h1+0.2)
77 pdf.set_font('Arial','', 14.0)
78 pdf.cell(pdf.w-0.5, 0.5, 'Template and non-template IsomiRs',align='C')
79 pdf.set_font('Arial', '', 11.0)
80 FPDF.set_y(pdf,h2)
81 FPDF.set_y(pdf,9.5)
82 # Image caption
83 pdf.cell(0.2)
84 if analysis=="2":
85 pdf.cell(3.0, 0.0, " Template, non-template, miRNA reference and unmapped sequences as percentage of total sRNA")
86 else:
87 pdf.cell(3.0, 0.0, " Template, miRNA reference and unmapped sequences as percentage of total sRNA")
88 pdf.ln(0.2)
89 pdf.cell(0.2)
90 pdf.cell(3.0, 0.0, " reads in Control (left) and treated (right) groups")
91
92
93
94 pdf.add_page()
95 pdf.set_font('Arial', 'B', 16.0)
96 pdf.cell(pdf.w-0.5, 0.5, "Reference form and isomiR among total miRNA reads",align='C')
97 pdf.ln(0.7)
98 pdf.set_font('Arial', 'B', 12.0)
99 pdf.cell(pdf.w-0.5, 0.5, "Template isomiR profile (redundant)",align='C')
100 pdf.ln(0.5)
101 pdf.image(images[3],x=1.5, w=5.5, h=4)
102 pdf.ln(0.6)
103 pdf.cell(pdf.w-0.5, 0.0, "Template isomiR profile (non-redundant)",align='C')
104 pdf.set_font('Arial', '', 12.0)
105 pdf.ln(0.2)
106 pdf.image(images[4],x=1.5, w=5.5, h=4)
107 pdf.ln(0.3)
108 pdf.set_font('Arial', '', 11.0)
109 pdf.cell(0.2)
110 pdf.cell(3.0, 0.0, " * IsomiRs potentialy initiated from multiple loci")
111
112
113 if analysis=="2":
114 pdf.add_page('L')
115
116 pdf.set_font('Arial', 'B', 16.0)
117 pdf.cell(pdf.w-0.5, 0.5, "Non-template IsomiRs",align='C')
118 pdf.ln(0.5)
119 pdf.set_font('Arial', 'B', 12.0)
120 pdf.cell(pdf.w-0.5, 0.5, "3' Additions of reference of isomiR sequence",align='C')
121 pdf.ln(0.7)
122
123 yh=FPDF.get_y(pdf)
124 pdf.image(images[5],x=1.5,w=3.65, h=2.65)
125 pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65)
126 pdf.ln(0.5)
127 yh=FPDF.get_y(pdf)
128 pdf.image(images[6],x=1.5,w=3.65, h=2.65)
129 pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65)
130
131 pdf.close()
132 pdf.output('report1.pdf','F')
133
134
135
136
137 #############################################################################################################################################################3
138
139 def pdf_after_DE(analysis,top):
140
141 # Import FPDF class
142 from fpdf import FPDF
143
144 # Import glob module to find all the files matching a pattern
145 import glob
146
147 # Image extensions
148 if analysis=="2":
149 image_extensions = ("tem.png","a2.png","non.png")
150 else:
151 image_extensions = ("tem.png","a2.png")
152
153 # This list will hold the images file names
154 images = []
155
156 # Build the image list by merging the glob results (a list of files)
157 # for each extension. We are taking images from current folder.
158 for extension in image_extensions:
159 images.extend(glob.glob(extension))
160 #sys.exit(images)
161 # Create instance of FPDF class
162 pdf = FPDF('P', 'in', 'letter')
163 # Add new page. Without this you cannot create the document.
164 pdf.add_page()
165 # Set font to Arial, 'B'old, 16 pts
166 pdf.set_font('Arial', 'B', 16.0)
167
168 # Page header
169 pdf.cell(pdf.w-0.5, 0.5, 'Differential expression of miRNAs and Isoforms',align='C')
170 #pdf.ln(0.25)
171
172 pdf.ln(0.7)
173 pdf.set_font('Arial','B', 12.0)
174 if "tem.png" in images:
175 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNA and template isoforms',align='C')
176 # Smaller font for image captions
177 pdf.set_font('Arial', '', 10.0)
178 # Image caption
179 pdf.ln(0.4)
180 pdf.image(images[images.index("tem.png")],x=0.8, w=7, h=8)
181 pdf.ln(0.3)
182 pdf.set_font('Arial','B', 12.0)
183 else:
184 print("WARNING: There aren't miRNAs which fullfiled these criteria" )
185
186 if "non.png" in images and analysis=="2":
187 if "tem.png" in images: pdf.add_page()
188 pdf.ln(0.7)
189 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed non-template isomiRs',align='C')
190 pdf.ln(0.4)
191 pdf.image(images[images.index("non.png")],x=0.5, w=7.5, h=6.5)
192 else:
193 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
194
195
196 if "a2.png" in images:
197 if len(images)>=2: pdf.add_page()
198 pdf.ln(0.5)
199 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNAs and isomiRs grouped by arm',align='C')
200 pdf.ln(0.4)
201 pdf.image(images[images.index("a2.png")],x=0.8, w=7, h=8)
202 pdf.ln(0.3)
203 else:
204 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
205
206
207 pdf.output('report2.pdf', 'F')
208
209
210