--- /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')
+
+
+