Example code to generate three renderings of a non-metabolic KEGG pathway, with important information in the .png.

kgml_ex2.py

import KGML_parser
from KGML_scrape import retrieve_KEGG_pathway
from KGML_vis import KGMLCanvas
from Bio.Graphics.ColorSpiral import ColorSpiral

# Get the ko03070 map from KEGG, and write it out to file, visualised as
# the .png, and as the elements from the KGML file
pathway = retrieve_KEGG_pathway('ko03070')
kgml_map = KGMLCanvas(pathway, show_maps=True)

# Let's use some arbitrary colours for the orthologs
cs = ColorSpiral(a=2, b=0.2, v_init=0.85, v_final=0.5, 
                 jitter=0.03)
# Loop over the orthologs in the pathway, and change the
# background colour
orthologs = [e for e in pathway.orthologs]
for o, c in zip(orthologs,
                cs.get_colors(len(orthologs))):
    for g in o.graphics:
        g.bgcolor = c
                              
# Default settings are for the KGML elements only
kgml_map.draw('ex2_kgml_render.pdf')

# We need to use the image map, and turn off the KGML elements, to see
# only the .png base map. We could have set these values on canvas
# instantiation
kgml_map.import_imagemap = True
kgml_map.show_maps = False
kgml_map.show_orthologs = False
kgml_map.draw_relations = False
kgml_map.show_compounds = False
kgml_map.show_genes = False
kgml_map.draw('ex2_png_render.pdf')

# And rendering elements as an overlay
kgml_map.show_compounds = True
kgml_map.show_genes = True
kgml_map.show_orthologs = True
kgml_map.draw('ex2_overlay_render.pdf')