|
8
|
1 # Import FPDF class
|
|
|
2 from fpdf import FPDF
|
|
|
3
|
|
|
4 # Import glob module to find all the files matching a pattern
|
|
|
5 import glob
|
|
|
6
|
|
|
7 def pdf_before_DE(analysis):
|
|
|
8
|
|
|
9 # Image extensions
|
|
|
10 if analysis=="2":
|
|
|
11 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")
|
|
|
12 else:
|
|
|
13 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png")
|
|
|
14 # This list will hold the images file names
|
|
|
15 images = []
|
|
|
16
|
|
|
17 # Build the image list by merging the glob results (a list of files)
|
|
|
18 # for each extension. We are taking images from current folder.
|
|
|
19 for extension in image_extensions:
|
|
|
20 images.extend(glob.glob(extension))
|
|
|
21
|
|
|
22 # Create instance of FPDF class
|
|
|
23 pdf = FPDF('P', 'in', 'A4')
|
|
|
24 # Add new page. Without this you cannot create the document.
|
|
|
25 pdf.add_page()
|
|
|
26 # Set font to Arial, 'B'old, 16 pts
|
|
|
27 pdf.set_font('Arial', 'B', 20.0)
|
|
|
28
|
|
|
29 # Page header
|
|
|
30 pdf.cell(pdf.w-0.5, 0.5, 'IsomiR Profile Report',align='C')
|
|
|
31 pdf.ln(0.7)
|
|
|
32 pdf.set_font('Arial','', 16.0)
|
|
|
33 pdf.cell(pdf.w-0.5, 0.5, 'sRNA Length Distribution',align='C')
|
|
|
34
|
|
|
35 # Smaller font for image captions
|
|
|
36 pdf.set_font('Arial', '', 11.0)
|
|
|
37
|
|
|
38 # Image caption
|
|
|
39 pdf.ln(0.5)
|
|
|
40
|
|
|
41 yh=FPDF.get_y(pdf)
|
|
|
42 pdf.image(images[0],x=0.3,w=4, h=3)
|
|
|
43 pdf.image(images[1],x=4,y=yh, w=4, h=3)
|
|
|
44 pdf.ln(0.3)
|
|
|
45
|
|
|
46 # Image caption
|
|
|
47 pdf.cell(0.2)
|
|
|
48 pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precussor arm reference DB (5p and 3p arms) in Control (left)")
|
|
|
49 pdf.ln(0.2)
|
|
|
50 pdf.cell(0.2)
|
|
|
51 pdf.cell(3.0, 0.0, " and Treated (right) groups")
|
|
|
52
|
|
|
53
|
|
|
54 pdf.ln(0.5)
|
|
|
55 h1=FPDF.get_y(pdf)
|
|
|
56 pdf.image(images[2],x=1, w=6.5, h=5)
|
|
|
57 h2=FPDF.get_y(pdf)
|
|
|
58 FPDF.set_y(pdf,h1+0.2)
|
|
|
59 pdf.set_font('Arial','', 14.0)
|
|
|
60 pdf.cell(pdf.w-0.5, 0.5, 'Template and non-template IsomiRs',align='C')
|
|
|
61 pdf.set_font('Arial', '', 11.0)
|
|
|
62 FPDF.set_y(pdf,h2)
|
|
|
63 FPDF.set_y(pdf,9.5)
|
|
|
64 # Image caption
|
|
|
65 pdf.cell(0.2)
|
|
|
66 if analysis=="2":
|
|
|
67 pdf.cell(3.0, 0.0, " Template, non-template, miRNA reference and unmapped sequences as percentage of total sRNA")
|
|
|
68 else:
|
|
|
69 pdf.cell(3.0, 0.0, " Template, miRNA reference and unmapped sequences as percentage of total sRNA")
|
|
|
70 pdf.ln(0.2)
|
|
|
71 pdf.cell(0.2)
|
|
|
72 pdf.cell(3.0, 0.0, " reads in Control (left) and treated (right) groups")
|
|
|
73
|
|
|
74
|
|
|
75
|
|
|
76 pdf.add_page()
|
|
|
77 pdf.set_font('Arial', 'B', 16.0)
|
|
|
78 pdf.cell(pdf.w-0.5, 0.5, "Reference form and isomiR among total miRNA reads",align='C')
|
|
|
79 pdf.ln(0.7)
|
|
|
80 pdf.set_font('Arial', 'B', 12.0)
|
|
|
81 pdf.cell(pdf.w-0.5, 0.5, "Template isomiR profile (redundant)",align='C')
|
|
|
82 pdf.ln(0.5)
|
|
|
83 pdf.image(images[3],x=1.5, w=5.5, h=4)
|
|
|
84 pdf.ln(0.6)
|
|
|
85 pdf.cell(pdf.w-0.5, 0.0, "Template isomiR profile (non-redundant)",align='C')
|
|
|
86 pdf.set_font('Arial', '', 12.0)
|
|
|
87 pdf.ln(0.2)
|
|
|
88 pdf.image(images[4],x=1.5, w=5.5, h=4)
|
|
|
89 pdf.ln(0.3)
|
|
|
90 pdf.set_font('Arial', '', 11.0)
|
|
|
91 pdf.cell(0.2)
|
|
|
92 pdf.cell(3.0, 0.0, " * IsomiRs potentialy initiated from multiple loci")
|
|
|
93
|
|
|
94
|
|
|
95 if analysis=="2":
|
|
|
96 pdf.add_page('L')
|
|
|
97
|
|
|
98 pdf.set_font('Arial', 'B', 16.0)
|
|
|
99 pdf.cell(pdf.w-0.5, 0.5, "Non-template IsomiRs",align='C')
|
|
|
100 pdf.ln(0.5)
|
|
|
101 pdf.set_font('Arial', 'B', 12.0)
|
|
|
102 pdf.cell(pdf.w-0.5, 0.5, "3' Additions of reference of isomiR sequence",align='C')
|
|
|
103 pdf.ln(0.7)
|
|
|
104
|
|
|
105 yh=FPDF.get_y(pdf)
|
|
|
106 pdf.image(images[5],x=1.5,w=3.65, h=2.65)
|
|
|
107 pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65)
|
|
|
108 pdf.ln(0.5)
|
|
|
109 yh=FPDF.get_y(pdf)
|
|
|
110 pdf.image(images[6],x=1.5,w=3.65, h=2.65)
|
|
|
111 pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65)
|
|
|
112
|
|
|
113 pdf.close()
|
|
|
114 pdf.output('report1.pdf','F')
|
|
|
115
|
|
|
116
|
|
|
117
|
|
|
118
|
|
|
119 #############################################################################################################################################################3
|
|
|
120
|
|
|
121 def pdf_after_DE(analysis,top,font_path,iso_star_fl,non_star_fl):
|
|
|
122
|
|
|
123 # Image extensions
|
|
|
124 if analysis=="2":
|
|
|
125 image_extensions = ("tem.png","a2.png","non.png")
|
|
|
126 else:
|
|
|
127 image_extensions = ("tem.png","a2.png")
|
|
|
128
|
|
|
129 # This list will hold the images file names
|
|
|
130 images = []
|
|
|
131
|
|
|
132 # Build the image list by merging the glob results (a list of files)
|
|
|
133 # for each extension. We are taking images from current folder.
|
|
|
134 for extension in image_extensions:
|
|
|
135 images.extend(glob.glob(extension))
|
|
|
136
|
|
|
137 # Create instance of FPDF class
|
|
|
138 pdf = FPDF('P', 'in', 'letter')
|
|
|
139 pdf.add_font('uni-arial', '', font_path+"/arial-unicode-ms.ttf", uni=True)
|
|
|
140 # Add new page. Without this you cannot create the document.
|
|
|
141 pdf.add_page()
|
|
|
142 # Set font to Arial, 'B'old, 16 pts
|
|
|
143 pdf.set_font('Arial', 'B', 16.0)
|
|
|
144
|
|
|
145 # Page header
|
|
|
146 pdf.cell(pdf.w-0.5, 0.5, 'Differential expression of miRNAs and isomiRs',align='C')
|
|
|
147 #pdf.ln(0.25)
|
|
|
148
|
|
|
149 pdf.ln(0.7)
|
|
|
150 pdf.set_font('Arial','B', 12.0)
|
|
|
151 if "tem.png" in images:
|
|
|
152 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed miRNA and templated isoforms',align='C')
|
|
|
153 # Smaller font for image captions
|
|
|
154 pdf.set_font('Arial', '', 10.0)
|
|
|
155 # Image caption
|
|
|
156 pdf.ln(0.4)
|
|
|
157 pdf.image(images[images.index("tem.png")],x=0.8, w=7, h=8)
|
|
|
158 pdf.ln(0.3)
|
|
|
159 if iso_star_fl==1:
|
|
|
160 pdf.set_font('uni-arial', '', 9.0)
|
|
|
161 pdf.cell(0.2)
|
|
|
162 pdf.cell(3.0, 0.0, " ★ IsomiRs potentially generated from multiple loci")
|
|
|
163 #pdf.set_font('Arial','B', 12.0)
|
|
|
164 else:
|
|
|
165 print("WARNING: There aren't miRNAs which fullfiled these criteria" )
|
|
|
166 pdf.set_font('Arial','B', 12.0)
|
|
|
167 if "non.png" in images and analysis=="2":
|
|
|
168 if "tem.png" in images: pdf.add_page()
|
|
|
169 pdf.ln(0.7)
|
|
|
170 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed non-templated isomiRs',align='C')
|
|
|
171 pdf.ln(0.4)
|
|
|
172 pdf.image(images[images.index("non.png")],x=0.8, w=7, h=8)
|
|
|
173 pdf.ln(0.3)
|
|
|
174 if non_star_fl==1:
|
|
|
175 pdf.set_font('uni-arial', '', 9.0)
|
|
|
176 pdf.cell(0.2)
|
|
|
177 pdf.cell(3.0, 0.0, " ★ IsomiRs potentially generated from multiple loci")
|
|
|
178
|
|
|
179 #pdf.image(images[images.index("non.png")],x=0.5, w=7.5, h=6.5)
|
|
|
180 else:
|
|
|
181 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
|
|
|
182
|
|
|
183 pdf.set_font('Arial','B', 12.0)
|
|
|
184 if "a2.png" in images:
|
|
|
185 if len(images)>=2: pdf.add_page()
|
|
|
186 pdf.ln(0.5)
|
|
|
187 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed miRNAs and isomiRs grouped by arm',align='C')
|
|
|
188 pdf.ln(0.4)
|
|
|
189 pdf.image(images[images.index("a2.png")],x=0.8, w=7, h=8)
|
|
|
190 pdf.ln(0.3)
|
|
|
191 else:
|
|
|
192 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
|
|
|
193
|
|
|
194
|
|
|
195 pdf.output('report2.pdf', 'F')
|
|
|
196
|
|
|
197
|
|
|
198
|
