# HG changeset patch # User glogobyte # Date 1634124006 0 # Node ID fa26ea53c0552e6ca2e7bfcaa607bcfe984920ab # Parent 77d835d85a2fb015d608fe50dd1561a6ad85715d Uploaded diff -r 77d835d85a2f -r fa26ea53c055 viz_graphs.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/viz_graphs.py Wed Oct 13 11:20:06 2021 +0000 @@ -0,0 +1,198 @@ + # Import FPDF class + from fpdf import FPDF + + # Import glob module to find all the files matching a pattern + import glob + +def pdf_before_DE(analysis): + + # Image extensions + if analysis=="2": + 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") + else: + image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png") + # This list will hold the images file names + images = [] + + # Build the image list by merging the glob results (a list of files) + # for each extension. We are taking images from current folder. + for extension in image_extensions: + images.extend(glob.glob(extension)) + + # Create instance of FPDF class + pdf = FPDF('P', 'in', 'A4') + # Add new page. Without this you cannot create the document. + pdf.add_page() + # Set font to Arial, 'B'old, 16 pts + pdf.set_font('Arial', 'B', 20.0) + + # Page header + pdf.cell(pdf.w-0.5, 0.5, 'IsomiR Profile Report',align='C') + pdf.ln(0.7) + pdf.set_font('Arial','', 16.0) + pdf.cell(pdf.w-0.5, 0.5, 'sRNA Length Distribution',align='C') + + # Smaller font for image captions + pdf.set_font('Arial', '', 11.0) + + # Image caption + pdf.ln(0.5) + + yh=FPDF.get_y(pdf) + pdf.image(images[0],x=0.3,w=4, h=3) + pdf.image(images[1],x=4,y=yh, w=4, h=3) + pdf.ln(0.3) + + # Image caption + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precussor arm reference DB (5p and 3p arms) in Control (left)") + pdf.ln(0.2) + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " and Treated (right) groups") + + + pdf.ln(0.5) + h1=FPDF.get_y(pdf) + pdf.image(images[2],x=1, w=6.5, h=5) + h2=FPDF.get_y(pdf) + FPDF.set_y(pdf,h1+0.2) + pdf.set_font('Arial','', 14.0) + pdf.cell(pdf.w-0.5, 0.5, 'Template and non-template IsomiRs',align='C') + pdf.set_font('Arial', '', 11.0) + FPDF.set_y(pdf,h2) + FPDF.set_y(pdf,9.5) + # Image caption + pdf.cell(0.2) + if analysis=="2": + pdf.cell(3.0, 0.0, " Template, non-template, miRNA reference and unmapped sequences as percentage of total sRNA") + else: + pdf.cell(3.0, 0.0, " Template, miRNA reference and unmapped sequences as percentage of total sRNA") + pdf.ln(0.2) + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " reads in Control (left) and treated (right) groups") + + + + pdf.add_page() + pdf.set_font('Arial', 'B', 16.0) + pdf.cell(pdf.w-0.5, 0.5, "Reference form and isomiR among total miRNA reads",align='C') + pdf.ln(0.7) + pdf.set_font('Arial', 'B', 12.0) + pdf.cell(pdf.w-0.5, 0.5, "Template isomiR profile (redundant)",align='C') + pdf.ln(0.5) + pdf.image(images[3],x=1.5, w=5.5, h=4) + pdf.ln(0.6) + pdf.cell(pdf.w-0.5, 0.0, "Template isomiR profile (non-redundant)",align='C') + pdf.set_font('Arial', '', 12.0) + pdf.ln(0.2) + pdf.image(images[4],x=1.5, w=5.5, h=4) + pdf.ln(0.3) + pdf.set_font('Arial', '', 11.0) + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " * IsomiRs potentialy initiated from multiple loci") + + + if analysis=="2": + pdf.add_page('L') + + pdf.set_font('Arial', 'B', 16.0) + pdf.cell(pdf.w-0.5, 0.5, "Non-template IsomiRs",align='C') + pdf.ln(0.5) + pdf.set_font('Arial', 'B', 12.0) + pdf.cell(pdf.w-0.5, 0.5, "3' Additions of reference of isomiR sequence",align='C') + pdf.ln(0.7) + + yh=FPDF.get_y(pdf) + pdf.image(images[5],x=1.5,w=3.65, h=2.65) + pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65) + pdf.ln(0.5) + yh=FPDF.get_y(pdf) + pdf.image(images[6],x=1.5,w=3.65, h=2.65) + pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65) + + pdf.close() + pdf.output('report1.pdf','F') + + + + +#############################################################################################################################################################3 + +def pdf_after_DE(analysis,top,font_path,iso_star_fl,non_star_fl): + + # Image extensions + if analysis=="2": + image_extensions = ("tem.png","a2.png","non.png") + else: + image_extensions = ("tem.png","a2.png") + + # This list will hold the images file names + images = [] + + # Build the image list by merging the glob results (a list of files) + # for each extension. We are taking images from current folder. + for extension in image_extensions: + images.extend(glob.glob(extension)) + + # Create instance of FPDF class + pdf = FPDF('P', 'in', 'letter') + pdf.add_font('uni-arial', '', font_path+"/arial-unicode-ms.ttf", uni=True) + # Add new page. Without this you cannot create the document. + pdf.add_page() + # Set font to Arial, 'B'old, 16 pts + pdf.set_font('Arial', 'B', 16.0) + + # Page header + pdf.cell(pdf.w-0.5, 0.5, 'Differential expression of miRNAs and isomiRs',align='C') + #pdf.ln(0.25) + + pdf.ln(0.7) + pdf.set_font('Arial','B', 12.0) + if "tem.png" in images: + pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed miRNA and templated isoforms',align='C') + # Smaller font for image captions + pdf.set_font('Arial', '', 10.0) + # Image caption + pdf.ln(0.4) + pdf.image(images[images.index("tem.png")],x=0.8, w=7, h=8) + pdf.ln(0.3) + if iso_star_fl==1: + pdf.set_font('uni-arial', '', 9.0) + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " ★ IsomiRs potentially generated from multiple loci") + #pdf.set_font('Arial','B', 12.0) + else: + print("WARNING: There aren't miRNAs which fullfiled these criteria" ) + pdf.set_font('Arial','B', 12.0) + if "non.png" in images and analysis=="2": + if "tem.png" in images: pdf.add_page() + pdf.ln(0.7) + pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed non-templated isomiRs',align='C') + pdf.ln(0.4) + pdf.image(images[images.index("non.png")],x=0.8, w=7, h=8) + pdf.ln(0.3) + if non_star_fl==1: + pdf.set_font('uni-arial', '', 9.0) + pdf.cell(0.2) + pdf.cell(3.0, 0.0, " ★ IsomiRs potentially generated from multiple loci") + + #pdf.image(images[images.index("non.png")],x=0.5, w=7.5, h=6.5) + else: + print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" ) + + pdf.set_font('Arial','B', 12.0) + if "a2.png" in images: + if len(images)>=2: pdf.add_page() + pdf.ln(0.5) + pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' differentially expressed miRNAs and isomiRs grouped by arm',align='C') + pdf.ln(0.4) + pdf.image(images[images.index("a2.png")],x=0.8, w=7, h=8) + pdf.ln(0.3) + else: + print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" ) + + + pdf.output('report2.pdf', 'F') + + +