It would be nice to separate 'graphical' and 'functional' parts of the code to separate functions. I know this is quite some work, but I also believe it would be worth from the perspective of readability.

[xiaoliz0]

          It would be nice to separate 'graphical' and 'functional' parts of the code to separate functions. I know this is quite some work, but I also believe it would be worth from the perspective of readability. 

Here is just a small example - lines 1432-1454 - a new function set_slide6_layout_parameters is defined below for dealing with various slide6 layout parameters and a new dictionary slide6_layout_params is defined to hold all the parameters in one data structure instead of all the different variables:

def set_slide6_layout_parameters(DNA_normal_sampleID, output_file_preMTB_table_path):
      layout_params = dict()

      if (DNA_normal_sampleID != ""):
            layout_params['table_header'] = ["Gene symbol", "Protein change", "Coding status", "VAF tumor DNA [0,1]", "VAF normal DNA"]
      else:
            layout_params['table_header'] = ["Gene symbol", "Protein change", "Coding status", "VAF tumor DNA [0,1]"]

      layout_params['table_data_file'] = output_file_preMTB_table_path + "_AllReporVariants_AltProtein.txt" 
      layout_params['table_pptSlide']  = [2,6,7]
      layout_params['table_name']      = "Variants that alter protein coding sequence "
      layout_params['header_left']     = 7.36
      layout_params['header_top']      = 0.82
      layout_params['header_width']    = 2.55
      layout_params['table_left']      = 7.23
      layout_params['table_top']       = 1.06
      layout_params['table_width']     = 2.76
      layout_params['table_height']    = 1.63
      layout_params['table_font_size'] = 7
      layout_params['if_print_rowNo']  = False

      return layout_params

then one can use the function in the main like in the last line here:

DNA_normal_sampleID="IPDXXXX-D01-X01-XXX"
output_file_preMTB_table_path="output_path/some_filename_prefix"
slide6_layout_params=dict()

slide6_layout_params = set_slide6_layout_parameters(DNA_normal_sampleID, output_file_preMTB_table_path)

and afterwards all the 'slide6' variables used as inputs in insert_table_to_ppt() can be reduced to 'slide6_layout_params' and read from the dictionary inside the function as needed.

Hopefully I did not forget any other place where the slide6 variables are used...

_Originally posted by @tinavisnovska in https://github.com/InPreD/PRONTO/pull/36#discussion_r1627452875_