Mercurial > repos > glogobyte > viztool
comparison viz_graphs.py @ 17:a09d238416ba draft
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author | glogobyte |
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date | Wed, 28 Oct 2020 07:42:50 +0000 |
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children |
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16:34ffe50a8da6 | 17:a09d238416ba |
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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 |