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 multiplicity_legend(ts):
ts.legend.add_face(ete3.faces.TextFace(""), 0)
ts.legend.add_face(ete3.faces.TextFace("Multiplicity"), 1)
for multiplicity in [1, 10, 100]:
size = scale_node(multiplicity)
pie_face = ete3.PieChartFace([100],
width=size,
height=size,
colors=['grey'])
ts.legend.add_face(pie_face, 0)
ts.legend.add_face(ete3.faces.TextFace(str(multiplicity)), 1)
def leaf_style(node, seqmeta, tp_colors, highlight_node=None):
name = node.name + " (mf={}) ".format(round(float(seqmeta['mut_freq']), 3))
F = ete3.faces.TextFace(name, fsize=9)
ete3.add_face_to_node(F, node, column=1, position='branch-right')
## Style the node with color corresponding to timepoint
nstyle = ete3.NodeStyle()
#if node.name == highlight_node:
#nstyle['fgcolor'] = 'brown'
#else:
#nstyle['fgcolor'] = tp_colors[seqmeta['timepoint']]
nstyle['size'] = 0
node.set_style(nstyle)
# Style the node with color corresponding to timepoint
if False:
nstyle = ete3.NodeStyle()
if node.name == highlight_node:
nstyle['fgcolor'] = 'brown'
else:
nstyle['fgcolor'] = tp_colors[seqmeta['timepoint']]
nstyle['size'] = 14
node.set_style(nstyle)
timepoints = filter(
lambda x: x,
seqmeta.get('cluster_timepoints', seqmeta['timepoints']).split(':'))
duplicities = [
int(n)
for n in seqmeta.get('cluster_timepoint_multiplicities',
seqmeta['timepoint_multiplicities']).split(':')
if n
]
multiplicity = int(
seqmeta.get('cluster_multiplicity', seqmeta['multiplicity']))
percents = [d * 100 / multiplicity for d in duplicities]
colors = [tp_colors[t] for t in timepoints]
pie_node = ete3.PieChartFace(percents,
width=scale_node(multiplicity),
height=scale_node(multiplicity),
colors=colors,
line_color='black')
ete3.add_face_to_node(pie_node, node, column=0)