--- a/viz_graphs.py	Fri Oct 15 08:54:12 2021 +0000
+++ b/viz_graphs.py	Wed Oct 20 08:45:05 2021 +0000
@@ -4,118 +4,6 @@
  # 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):
@@ -184,7 +72,7 @@
   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.cell(pdf.w-0.5, 0.5, '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)