Skip to content

Commit

Permalink
PEP8 corrections to KGML_vis.py
Browse files Browse the repository at this point in the history
  • Loading branch information
@widdowquinn
widdowquinn committed Feb 3, 2014
1 parent af2f772 commit 6866257
Showing 1 changed file with 43 additions and 56 deletions.
99 changes: 43 additions & 56 deletions KGML_vis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@

""" This module provides classes and functions to visualise a KGML Pathway Map
The KGML definition is as of release KGML v0.7.1
The KGML definition is as of release KGML v0.7.1
(http://www.kegg.jp/kegg/xml/docs/)
Classes:
Expand All @@ -50,15 +50,17 @@
import StringIO
import tempfile


def hexdarken(hexcolour, factor=0.7):
""" Take a passed hex colour and return an RGB colour that is
""" Take a passed hex colour and return an RGB colour that is
slightly darker (if possible)
"""
c = colors.HexColor(hexcolour)
for a in ['red', 'green', 'blue']:
setattr(c, a, factor * getattr(c, a))
return c



def get_temp_imagefilename(url):
""" Create a new temporary file to hold the image file at the passed URL,
and return the filename
Expand All @@ -71,7 +73,7 @@ def get_temp_imagefilename(url):
f.close()
im.save(fname, 'PNG')
return fname


class KGMLCanvas(object):
""" Contains a Reportlab Canvas-based representation of a KGML pathway map
Expand All @@ -96,8 +98,8 @@ def __init__(self, pathway, import_imagemap=False, label_compounds=True,
self.fontsize = fontsize
self.draw_relations = draw_relations
self.non_reactant_transparency = 0.3
self.import_imagemap = import_imagemap # Import the map .png from URL
# percentage of canvas that will be margin in on either side in the
self.import_imagemap = import_imagemap # Import the map .png from URL
# percentage of canvas that will be margin in on either side in the
# X and Y directions
self.margins = margins

Expand All @@ -122,11 +124,11 @@ def draw(self, filename):
self.pathway.bounds[1][1])
# Instantiate canvas
self.drawing = \
canvas.Canvas(filename, bottomup=0,
pagesize=(cwidth * \
(1 + 2 * self.margins[0]),
cheight * \
(1 + 2 * self.margins[1])))
canvas.Canvas(filename, bottomup=0,
pagesize=(cwidth *
(1 + 2 * self.margins[0]),
cheight *
(1 + 2 * self.margins[1])))
self.drawing.setFont(self.fontname, self.fontsize)
# Transform the canvas to add the margins
self.drawing.translate(self.margins[0] * self.pathway.bounds[1][0],
Expand All @@ -139,7 +141,7 @@ def draw(self, filename):
self.drawing.drawImage(imfilename, 0, 0)
self.drawing.restoreState()
# Add the reactions, compounds and maps
# Maps go on first, to be overlaid by more information.
# Maps go on first, to be overlaid by more information.
# By default, they're slightly transparent.
if self.show_maps:
self.__add_maps()
Expand All @@ -150,18 +152,16 @@ def draw(self, filename):
self.__add_compounds()
if self.show_genes:
self.__add_genes()
#if self.draw_relations:
# self.__add_relations()
# Write the pathway map to PDF
self.drawing.save()

def __add_maps(self):
""" Adds maps to the drawing of the map
We do this first, as they're regional labels to be overlaid by
We do this first, as they're regional labels to be overlaid by
information. Also, we want to set the colour to something subtle.
We're using Hex colours because that's what KGML uses, and
We're using Hex colours because that's what KGML uses, and
Reportlab doesn't mind.
"""
for m in self.pathway.maps:
Expand All @@ -176,7 +176,7 @@ def __add_maps(self):
def __add_graphics(self, graphics):
""" Adds the passed graphics object to the map
Add text, add after the graphics object, for
Add text, add after the graphics object, for
sane Z-ordering
"""
if graphics.type == 'line':
Expand All @@ -190,7 +190,7 @@ def __add_graphics(self, graphics):
self.drawing.setLineWidth(1)
p.moveTo(x, y)
for (x, y) in graphics.coords:
p.lineTo(x,y)
p.lineTo(x, y)
self.drawing.drawPath(p)
self.drawing.setLineWidth(1) # Return to default
# KGML defines the (x, y) coordinates as the centre of the circle/
Expand All @@ -200,13 +200,13 @@ def __add_graphics(self, graphics):
self.drawing.circle(graphics.x, graphics.y, graphics.width*0.5,
stroke=1, fill=1)
elif graphics.type == 'roundrectangle':
self.drawing.roundRect(graphics.x - graphics.width * 0.5,
self.drawing.roundRect(graphics.x - graphics.width * 0.5,
graphics.y - graphics.height * 0.5,
graphics.width, graphics.height,
min(graphics.width, graphics.height) * 0.1,
stroke=1, fill=1)
elif graphics.type == 'rectangle':
self.drawing.rect(graphics.x - graphics.width * 0.5,
self.drawing.rect(graphics.x - graphics.width * 0.5,
graphics.y - graphics.height * 0.5,
graphics.width, graphics.height,
stroke=1, fill=1)
Expand All @@ -219,9 +219,9 @@ def __add_labels(self, graphics):
"""
if graphics.type == 'line':
# We use the midpoint of the line - sort of - we take the median
# line segment (list-wise, not in terms of length), and use the
# midpoint of that line. We could have other options here,
# maybe even parameterising it to a proportion of the total line
# line segment (list-wise, not in terms of length), and use the
# midpoint of that line. We could have other options here,
# maybe even parameterising it to a proportion of the total line
# length.
mid_idx = len(graphics.coords) * 0.5
if not int(mid_idx) == mid_idx:
Expand All @@ -245,9 +245,9 @@ def __add_labels(self, graphics):
text = graphics.name[:12] + '...'
self.drawing.drawCentredString(x, y, text)
self.drawing.setFont(self.fontname, self.fontsize)

def __add_orthologs(self):
""" Adds 'ortholog' Entry elements to the drawing of the map.
""" Adds 'ortholog' Entry elements to the drawing of the map.
In KGML, these are typically line objects, so we render them
before the compound circles to cover the unsightly ends/junctions
Expand All @@ -264,8 +264,8 @@ def __add_orthologs(self):
self.__add_labels(g)

def __add_reaction_entries(self):
""" Adds Entry elements corresponding to Reactions to the drawing of
the map.
""" Adds Entry elements corresponding to Reactions to the drawing of
the map.
In KGML, these are typically line objects, so we render them
before the compound circles to cover the unsightly ends/junctions
Expand Down Expand Up @@ -297,7 +297,7 @@ def __add_compounds(self):
if self.label_compounds:
if not compound.is_reactant:
t = 0.3
else:
else:
t = 1
self.drawing.setFillColor(colors.Color(0.2, 0.2, 0.2, t))
self.__add_labels(g)
Expand All @@ -314,20 +314,19 @@ def __add_genes(self):
if self.label_compounds:
self.drawing.setFillColor(hexdarken(g.fgcolor))
self.__add_labels(g)


def __add_relations(self):
""" Adds relations to the map
This is tricky. There is no defined graphic in KGML for a
This is tricky. There is no defined graphic in KGML for a
relation, and the corresponding entries are typically defined
as objects 'to be connected somehow'. KEGG uses KegSketch, which
is not public, and most third-party software draws straight line
arrows, with heads to indicate the appropriate direction
(at both ends for reversible reactions), using solid lines for
(at both ends for reversible reactions), using solid lines for
ECrel relation types, and dashed lines for maplink relation types.
The relation has:
The relation has:
entry1: 'from' node
entry2: 'to' node
subtype: what the relation refers to
Expand All @@ -338,7 +337,7 @@ def __add_relations(self):
# Dashed lines for maplinks, solid for everything else
for relation in list(self.pathway.relations):
if relation.type == 'maplink':
self.drawing.setDash(6,3)
self.drawing.setDash(6, 3)
else:
self.drawing.setDash()
for s in relation.subtypes:
Expand All @@ -361,41 +360,33 @@ def __draw_arrow(self, g_from, g_to):
centre_to = (0.5 * (bounds_to[0][0] + bounds_to[1][0]),
0.5 * (bounds_to[0][1] + bounds_to[1][1]))
p = self.drawing.beginPath()
#print True, g_from.name, g_to.name, bounds_to, bounds_from
# If the 'from' and 'to' graphics are vertically-aligned, draw a line
# from the 'from' to the 'to' entity
if bounds_to[0][0] < centre_from[0] < bounds_to[1][0]:
#print True, g_from.name, g_to.name, bounds_to, bounds_from
if centre_to[1] > centre_from[1]: # to above from
if centre_to[1] > centre_from[1]: # to above from
p.moveTo(centre_from[0], bounds_from[1][1])
p.lineTo(centre_from[0], bounds_to[0][1])
# Draw arrow point
else: # to below from
else: # to below from
p.moveTo(centre_from[0], bounds_from[0][1])
p.lineTo(centre_from[0], bounds_to[1][1])
# Draw arrow point
# Draw arrow point
elif bounds_from[0][0] < centre_to[0] < bounds_from[1][0]:
print True, g_from.name, g_to.name, bounds_to, bounds_from
if centre_to[1] > centre_from[1]: # to above from
if centre_to[1] > centre_from[1]: # to above from
p.moveTo(centre_to[0], bounds_from[1][1])
p.lineTo(centre_to[0], bounds_to[0][1])
# Draw arrow point
else: # to below from
else: # to below from
p.moveTo(centre_to[0], bounds_from[0][1])
p.lineTo(centre_to[0], bounds_to[1][1])
# Draw arrow point
# Draw arrow point
self.drawing.drawPath(p) # Draw arrow shaft
#print g_from
#print bounds_from
#print g_to
#print bounds_to




if __name__ == '__main__':
# Test production of Reportlab Canvas PDF visualisation
# Try a default KO metabolic map with ortholog lines given
# Try a default KO metabolic map with ortholog lines given
pathway = KGML_parser.read(open('ko01100.xml', 'rU'))
print pathway
kgml_map = KGMLCanvas(pathway)
Expand All @@ -412,7 +403,7 @@ def __draw_arrow(self, g_from, g_to):
g.width = 3
kgml_map.draw('KGML_canvas_ddc_test.pdf')

# Try a KO metabolic map with no ortholog lines, using a local .png
# Try a KO metabolic map with no ortholog lines, using a local .png
pathway = KGML_parser.read(open('ko_metabolic/ko00910.xml', 'rU'))
pathway.image = 'map/map00910.png'
print pathway
Expand All @@ -421,15 +412,15 @@ def __draw_arrow(self, g_from, g_to):
kgml_map.show_maps = False
kgml_map.draw('KGML_canvas_map_local_test.pdf')

# Try a KO metabolic map with no ortholog lines, using the KEGG .png
# Try a KO metabolic map with no ortholog lines, using the KEGG .png
pathway = KGML_parser.read(open('ko_metabolic/ko00253.xml', 'rU'))
print pathway
kgml_map = KGMLCanvas(pathway)
kgml_map.import_imagemap = True
kgml_map.show_maps = False
kgml_map.draw('KGML_canvas_map_test.pdf')

# Try a KO metabolic map with no ortholog lines using the KEGG .png,
# Try a KO metabolic map with no ortholog lines using the KEGG .png,
# but this time using a Dickeya XML file
pathway = KGML_parser.read(open('dda00190.xml', 'rU'))
print pathway
Expand All @@ -438,15 +429,11 @@ def __draw_arrow(self, g_from, g_to):
kgml_map.show_maps = True
kgml_map.draw('KGML_canvas_dda_map_test.pdf')

# Try a KO metabolic map with no ortholog lines using the KEGG .png,
# Try a KO metabolic map with no ortholog lines using the KEGG .png,
# but this time using a Dickeya XML file
pathway = KGML_parser.read(open('test_retrieve_ddc00190.kgml', 'rU'))
print pathway
kgml_map = KGMLCanvas(pathway)
kgml_map.import_imagemap = True
kgml_map.show_maps = True
kgml_map.draw('KGML_canvas_ddc_map_test.pdf')




0 comments on commit 6866257

Please sign in to comment.