def set_node_style(node, status, n_gl_sets, ref_label=None):
if status != 'internal':
if status not in scolors:
raise Exception('status \'%s\' not in scolors' % status)
node.img_style['bgcolor'] = scolors[status]
if status not in used_colors:
used_colors[status] = scolors[status]
if glutils.is_novel(node.name):
node.add_face(ete3.CircleFace(args.novel_dot_size, scolors['novel']), column=1) #, position='float') # if args.leaf_names else 'branch')
# linewidth = 2
# node.img_style['hz_line_width'] = linewidth
# node.img_style['vt_line_width'] = linewidth
names = status.split('-&-')
if node.is_leaf():
if args.pie_chart_faces and len(names) > 1:
pcf = ete3.PieChartFace(percents=[100./len(names) for _ in range(len(names))], width=args.leafheight, height=args.leafheight, colors=[scolors[n] for n in names], line_color=None)
# pcf = ete3.StackedBarFace(percents=[100./len(names) for _ in range(len(names))], width=30, height=50, colors=[scolors[n] for n in names], line_color=None)
node.add_face(pcf, column=0, position='aligned')
elif len(names) == 1 and names[0] in used_faces:
node.add_face(ete3.RectFace(width=5, height=args.leafheight, bgcolor=used_faces[names[0]], fgcolor=None), column=0, position='aligned')
elif n_gl_sets > 2:
rectnames = [n for n in names if n in used_faces]
node.add_face(ete3.StackedBarFace(percents=[100./len(names) for _ in range(len(rectnames))], width=5 * len(rectnames), height=args.leafheight, colors=[used_faces[rn] for rn in rectnames], line_color=None), column=0, position='aligned')
else: # every leaf has to have a face, so that every leaf takes up the same vertical space
node.add_face(ete3.RectFace(width=1, height=args.leafheight, bgcolor=None, fgcolor=None), column=0, position='aligned')
def write_legend(plotdir):
def get_leg_name(status):
if args.legends is not None and status in args.glslabels:
lname = args.legends[args.glslabels.index(status)]
elif status == 'both':
if len(args.glsfnames) == 2:
lname = 'both'
elif len(args.glsfnames) == 3:
lname = 'two'
else:
raise Exception('wtf %d' % len(args.glsfnames))
elif status == 'all':
if len(args.glsfnames) == 2:
lname = 'both'
elif len(args.glsfnames) == 3:
lname = 'all three'
else:
raise Exception('wtf %d' % len(args.glsfnames))
else:
lname = status
return lname
def add_stuff(status, leg_name, color):
legfo[leg_name] = color
if status in used_faces:
facefo[leg_name] = used_faces[status]
legfo, facefo = {}, {}
if args.ref_label is not None:
for status, color in simu_colors.items():
add_stuff(status, status, color)
else:
added_two_method_color = False
for status, color in used_colors.items():
if '-&-' in status:
for substatus in status.split(
'-&-'
): # arg, have to handle cases where the single one isn't in there
if get_leg_name(substatus) not in legfo:
add_stuff(substatus, get_leg_name(substatus),
scolors[substatus])
if not added_two_method_color:
leg_name = get_leg_name('both')
added_two_method_color = True
else:
continue
else:
leg_name = get_leg_name(status)
add_stuff(status, leg_name, color)
# figure out the order we want 'em in
lnames = sorted(legfo.keys())
for status in ['both', 'all']:
if get_leg_name(status) in lnames:
lnames.remove(get_leg_name(status))
lnames.append(get_leg_name(status))
etree = ete3.ClusterTree() #'(a);')
tstyle = ete3.TreeStyle()
tstyle.show_scale = False
# tstyle.show_leaf_name = False
# for node in etree.traverse():
# print node.name
# node.add_face(ete3.CircleFace(args.novel_dot_size, scolors['novel']), column=1) #, position='float') # if args.leaf_names else 'branch')
dummy_column = 0
pic_column = 1
text_column = 2
leg_title_height = 1.5 * args.leafheight # if args.legend_title is not None else 0.75 * args.leafheight
for icol in range(text_column + 1): # add a top border
tstyle.title.add_face(ete3.RectFace(0.9 * args.leafheight,
0.9 * args.leafheight,
fgcolor=None,
bgcolor=None),
column=icol)
tstyle.title.add_face(ete3.TextFace(' ', fsize=leg_title_height),
column=dummy_column) # adds a left border
if args.legend_title is not None:
tstyle.title.add_face(
ete3.TextFace('', fsize=leg_title_height), column=pic_column
) # keeps the first legend entry from getting added on this line
tstyle.title.add_face(
ete3.TextFace(args.legend_title,
fsize=leg_title_height,
fgcolor='black',
bold=True),
column=text_column
) # add an empty title so there's some white space at the top, even with no actual title text
for leg_name in lnames:
color = legfo[leg_name]
size_factor = 2.
if leg_name in facefo:
tstyle.title.add_face(
ete3.StackedBarFace([80., 20.],
width=size_factor * args.leafheight,
height=size_factor * args.leafheight,
colors=[color, facefo[leg_name]],
line_color='black'),
column=pic_column
) # looks like maybe they reversed fg/bg kwarg names
else:
tstyle.title.add_face(
ete3.RectFace(size_factor * args.leafheight,
size_factor * args.leafheight,
fgcolor='black',
bgcolor=color),
column=pic_column
) # looks like maybe they reversed fg/bg kwarg names
tstyle.title.add_face(ete3.TextFace(' ' + leg_name,
fsize=args.leafheight,
fgcolor='black'),
column=text_column)
tstyle.title.add_face(ete3.CircleFace(1.5 * args.novel_dot_size,
scolors['novel']),
column=pic_column)
tstyle.title.add_face(
ete3.TextFace('novel allele', fsize=args.leafheight),
column=text_column
) # keeps the first legend entry from getting added on this line
etree.render(plotdir + '/legend.svg', tree_style=tstyle)