Mercurial > repos > glogobyte > viztool
comparison viz_graphs.py @ 8:edec16f9566a draft
Uploaded
| author | glogobyte |
|---|---|
| date | Fri, 16 Oct 2020 18:16:06 +0000 |
| parents | |
| children |
comparison
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| 7:2c5723e2421a | 8:edec16f9566a |
|---|---|
| 1 import sys | |
| 2 def pdf_before_DE(analysis): | |
| 3 | |
| 4 # Import FPDF class | |
| 5 from fpdf import FPDF, fpdf | |
| 6 | |
| 7 # Import glob module to find all the files matching a pattern | |
| 8 import glob | |
| 9 | |
| 10 # Image extensions | |
| 11 if analysis=="2": | |
| 12 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") | |
| 13 else: | |
| 14 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png") | |
| 15 # This list will hold the images file names | |
| 16 images = [] | |
| 17 | |
| 18 # Build the image list by merging the glob results (a list of files) | |
| 19 # for each extension. We are taking images from current folder. | |
| 20 for extension in image_extensions: | |
| 21 images.extend(glob.glob(extension)) | |
| 22 #sys.exit(images) | |
| 23 # Create instance of FPDF class | |
| 24 pdf = FPDF('P', 'in', 'A4') | |
| 25 # Add new page. Without this you cannot create the document. | |
| 26 pdf.add_page() | |
| 27 # Set font to Arial, 'B'old, 16 pts | |
| 28 pdf.set_font('Arial', 'B', 20.0) | |
| 29 | |
| 30 # Page header | |
| 31 pdf.cell(pdf.w-0.5, 0.5, 'IsomiR Profile Report',align='C') | |
| 32 pdf.ln(0.7) | |
| 33 pdf.set_font('Arial','', 16.0) | |
| 34 pdf.cell(pdf.w-0.5, 0.5, 'sRNA Length Distribution',align='C') | |
| 35 | |
| 36 # Smaller font for image captions | |
| 37 pdf.set_font('Arial', '', 11.0) | |
| 38 | |
| 39 # Image caption | |
| 40 pdf.ln(0.5) | |
| 41 | |
| 42 yh=FPDF.get_y(pdf) | |
| 43 pdf.image(images[0],x=0.3,w=4, h=3) | |
| 44 pdf.image(images[1],x=4,y=yh, w=4, h=3) | |
| 45 pdf.ln(0.3) | |
| 46 | |
| 47 # Image caption | |
| 48 pdf.cell(0.2) | |
| 49 pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precussor arm reference DB (5p and 3p arms) in Control (left)") | |
| 50 pdf.ln(0.2) | |
| 51 pdf.cell(0.2) | |
| 52 pdf.cell(3.0, 0.0, " and Treated (right) groups") | |
| 53 | |
| 54 | |
| 55 pdf.ln(0.5) | |
| 56 h1=FPDF.get_y(pdf) | |
| 57 pdf.image(images[2],x=1, w=6.5, h=5) | |
| 58 h2=FPDF.get_y(pdf) | |
| 59 FPDF.set_y(pdf,h1+0.2) | |
| 60 pdf.set_font('Arial','', 14.0) | |
| 61 pdf.cell(pdf.w-0.5, 0.5, 'Template and non-template IsomiRs',align='C') | |
| 62 pdf.set_font('Arial', '', 11.0) | |
| 63 FPDF.set_y(pdf,h2) | |
| 64 FPDF.set_y(pdf,9.5) | |
| 65 # Image caption | |
| 66 pdf.cell(0.2) | |
| 67 if analysis=="2": | |
| 68 pdf.cell(3.0, 0.0, " Template, non-template, miRNA reference and unmapped sequences as percentage of total sRNA") | |
| 69 else: | |
| 70 pdf.cell(3.0, 0.0, " Template, miRNA reference and unmapped sequences as percentage of total sRNA") | |
| 71 pdf.ln(0.2) | |
| 72 pdf.cell(0.2) | |
| 73 pdf.cell(3.0, 0.0, " reads in Control (left) and treated (right) groups") | |
| 74 | |
| 75 | |
| 76 | |
| 77 pdf.add_page() | |
| 78 pdf.set_font('Arial', 'B', 16.0) | |
| 79 pdf.cell(pdf.w-0.5, 0.5, "Reference form and isomiR among total miRNA reads",align='C') | |
| 80 pdf.ln(0.7) | |
| 81 pdf.set_font('Arial', 'B', 12.0) | |
| 82 pdf.cell(pdf.w-0.5, 0.5, "Template isomiR profile (redundant)",align='C') | |
| 83 pdf.ln(0.5) | |
| 84 pdf.image(images[3],x=1.5, w=5.5, h=4) | |
| 85 pdf.ln(0.6) | |
| 86 pdf.cell(pdf.w-0.5, 0.0, "Template isomiR profile (non-redundant)",align='C') | |
| 87 pdf.set_font('Arial', '', 12.0) | |
| 88 pdf.ln(0.2) | |
| 89 pdf.image(images[4],x=1.5, w=5.5, h=4) | |
| 90 pdf.ln(0.3) | |
| 91 pdf.set_font('Arial', '', 11.0) | |
| 92 pdf.cell(0.2) | |
| 93 pdf.cell(3.0, 0.0, " * IsomiRs potentialy initiated from multiple loci") | |
| 94 | |
| 95 | |
| 96 if analysis=="2": | |
| 97 pdf.add_page('L') | |
| 98 | |
| 99 pdf.set_font('Arial', 'B', 16.0) | |
| 100 pdf.cell(pdf.w-0.5, 0.5, "Non-template IsomiRs",align='C') | |
| 101 pdf.ln(0.5) | |
| 102 pdf.set_font('Arial', 'B', 12.0) | |
| 103 pdf.cell(pdf.w-0.5, 0.5, "3' Additions of reference of isomiR sequence",align='C') | |
| 104 pdf.ln(0.7) | |
| 105 | |
| 106 yh=FPDF.get_y(pdf) | |
| 107 pdf.image(images[5],x=1.5,w=3.65, h=2.65) | |
| 108 pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65) | |
| 109 pdf.ln(0.5) | |
| 110 yh=FPDF.get_y(pdf) | |
| 111 pdf.image(images[6],x=1.5,w=3.65, h=2.65) | |
| 112 pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65) | |
| 113 | |
| 114 pdf.close() | |
| 115 pdf.output('report1.pdf','F') | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 #############################################################################################################################################################3 | |
| 121 | |
| 122 def pdf_after_DE(analysis,top): | |
| 123 | |
| 124 # Import FPDF class | |
| 125 from fpdf import FPDF | |
| 126 | |
| 127 # Import glob module to find all the files matching a pattern | |
| 128 import glob | |
| 129 | |
| 130 # Image extensions | |
| 131 if analysis=="2": | |
| 132 image_extensions = ("tem.png","a2.png","non.png") | |
| 133 else: | |
| 134 image_extensions = ("tem.png","a2.png") | |
| 135 | |
| 136 # This list will hold the images file names | |
| 137 images = [] | |
| 138 | |
| 139 # Build the image list by merging the glob results (a list of files) | |
| 140 # for each extension. We are taking images from current folder. | |
| 141 for extension in image_extensions: | |
| 142 images.extend(glob.glob(extension)) | |
| 143 #sys.exit(images) | |
| 144 # Create instance of FPDF class | |
| 145 pdf = FPDF('P', 'in', 'letter') | |
| 146 # Add new page. Without this you cannot create the document. | |
| 147 pdf.add_page() | |
| 148 # Set font to Arial, 'B'old, 16 pts | |
| 149 pdf.set_font('Arial', 'B', 16.0) | |
| 150 | |
| 151 # Page header | |
| 152 pdf.cell(pdf.w-0.5, 0.5, 'Differential expression of miRNAs and Isoforms',align='C') | |
| 153 #pdf.ln(0.25) | |
| 154 | |
| 155 pdf.ln(0.7) | |
| 156 pdf.set_font('Arial','B', 12.0) | |
| 157 if "tem.png" in images: | |
| 158 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNA and template isoforms',align='C') | |
| 159 # Smaller font for image captions | |
| 160 pdf.set_font('Arial', '', 10.0) | |
| 161 # Image caption | |
| 162 pdf.ln(0.4) | |
| 163 pdf.image(images[images.index("tem.png")],x=0.8, w=7, h=8) | |
| 164 pdf.ln(0.3) | |
| 165 pdf.set_font('Arial','B', 12.0) | |
| 166 else: | |
| 167 print("WARNING: There aren't miRNAs which fullfiled these criteria" ) | |
| 168 | |
| 169 if "non.png" in images and analysis=="2": | |
| 170 if "tem.png" in images: pdf.add_page() | |
| 171 pdf.ln(0.7) | |
| 172 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed non-template isomiRs',align='C') | |
| 173 pdf.ln(0.4) | |
| 174 pdf.image(images[images.index("non.png")],x=0.5, w=7.5, h=6.5) | |
| 175 else: | |
| 176 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" ) | |
| 177 | |
| 178 | |
| 179 if "a2.png" in images: | |
| 180 if len(images)>=2: pdf.add_page() | |
| 181 pdf.ln(0.5) | |
| 182 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNAs and isomiRs grouped by arm',align='C') | |
| 183 pdf.ln(0.4) | |
| 184 pdf.image(images[images.index("a2.png")],x=0.8, w=7, h=8) | |
| 185 pdf.ln(0.3) | |
| 186 else: | |
| 187 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" ) | |
| 188 | |
| 189 | |
| 190 pdf.output('report2.pdf', 'F') | |
| 191 | |
| 192 | |
| 193 |