def test_Bezier():
glyph = Bezier()
assert glyph.x0 == "x0"
assert glyph.y0 == "y0"
assert glyph.x1 == "x1"
assert glyph.y1 == "y1"
assert glyph.cx0 == "cx0"
assert glyph.cy0 == "cy0"
assert glyph.cx1 == "cx1"
assert glyph.cy1 == "cy1"
yield check_line, glyph
yield check_props, glyph, [
"x0", "y0", "x1", "y1", "cx0", "cy0", "cx1", "cy1"
], LINE
def yield_renderers(self):
"""Use the marker glyphs to display the arcs and beziers.
Takes reference points from data loaded at the ColumnDataSource.
"""
beziers = Bezier(x0='start_x',
y0='start_y',
x1='end_x',
y1='end_y',
cx0='cx0',
cy0='cy0',
cx1='cx1',
cy1='cy1',
line_alpha='weight',
line_color='colors')
yield GlyphRenderer(data_source=self.connection_data, glyph=beziers)
arcs = Arc(x=0,
y=0,
radius=1,
line_width=10,
start_angle='start_angle',
end_angle='end_angle',
line_color='line_color')
yield GlyphRenderer(data_source=self.arcs_data, glyph=arcs)
if self.label:
text_props = {
"text_color": "#000000",
"text_font_size": "8pt",
"text_align": "left",
"text_baseline": "middle"
}
labels = Text(x='text_x',
y='text_y',
text='text',
angle='angles',
**text_props
)
yield GlyphRenderer(data_source=self.text_data, glyph=labels)
def test_Bezier() -> None:
glyph = Bezier()
assert glyph.x0 == field("x0")
assert glyph.y0 == field("y0")
assert glyph.x1 == field("x1")
assert glyph.y1 == field("y1")
assert glyph.cx0 == field("cx0")
assert glyph.cy0 == field("cy0")
assert glyph.cx1 == field("cx1")
assert glyph.cy1 == field("cy1")
check_line_properties(glyph)
check_properties_existence(glyph, [
"x0",
"y0",
"x1",
"y1",
"cx0",
"cy0",
"cx1",
"cy1",
], LINE, GLYPH)
def test_Bezier():
glyph = Bezier()
assert glyph.x0 is None
assert glyph.y0 is None
assert glyph.x1 is None
assert glyph.y1 is None
assert glyph.cx0 is None
assert glyph.cy0 is None
assert glyph.cx1 is None
assert glyph.cy1 is None
check_line_properties(glyph)
check_properties_existence(glyph, [
"x0",
"y0",
"x1",
"y1",
"cx0",
"cy0",
"cx1",
"cy1",
], LINE, GLYPH)
def test_Bezier():
glyph = Bezier()
assert glyph.x0 is None
assert glyph.y0 is None
assert glyph.x1 is None
assert glyph.y1 is None
assert glyph.cx0 is None
assert glyph.cy0 is None
assert glyph.cx1 is None
assert glyph.cy1 is None
yield check_line, glyph
yield (check_props, glyph, [
"x0",
"y0",
"x1",
"y1",
"cx0",
"cy0",
"cx1",
"cy1",
], LINE)
def draw_line(scene: Plot, start: tuple, ctrl1: tuple, ctrl2: tuple,
end: tuple, is_curved: bool, edge_color: tuple):
if is_curved: # cubic Bezier curve
glyph = Bezier(
x0=start[0],
y0=start[1],
x1=end[0],
y1=end[1],
cx0=ctrl1[0],
cy0=ctrl1[1],
cx1=ctrl2[0],
cy1=ctrl2[1],
line_color='#{0:02x}{1:02x}{2:02x}'.format(*edge_color),
line_width=1)
scene.add_glyph(glyph)
else:
source = ColumnDataSource(
dict(x=[start[0], end[0]], y=[start[1], end[1]]))
glyph = Line(
x="x",
y="y",
line_width=1,
line_color='#{0:02x}{1:02x}{2:02x}'.format(*edge_color))
scene.add_glyph(source, glyph)
xm01=x - 0.1,
yp01=y + 0.2,
ym01=y - 0.2,
))
plot = Plot(title=None,
plot_width=300,
plot_height=300,
min_border=0,
toolbar_location=None)
glyph = Bezier(x0="x",
y0="y",
x1="xp02",
y1="y",
cx0="xp01",
cy0="yp01",
cx1="xm01",
cy1="ym01",
line_color="#d95f02",
line_width=2)
plot.add_glyph(source, glyph)
xaxis = LinearAxis()
plot.add_layout(xaxis, 'below')
yaxis = LinearAxis()
plot.add_layout(yaxis, 'left')
plot.add_layout(Grid(dimension=0, ticker=xaxis.ticker))
plot.add_layout(Grid(dimension=1, ticker=yaxis.ticker))
outer_radius=screen(20),
fill_color="#7FC97F")),
("arc",
Arc(x="x",
y="y",
radius=screen(20),
start_angle=0.6,
end_angle=4.1,
line_color="#BEAED4",
line_width=3)),
("bezier",
Bezier(x0="x",
y0="y",
x1="xp02",
y1="y",
cx0="xp01",
cy0="yp01",
cx1="xm01",
cy1="ym01",
line_color="#D95F02",
line_width=2)),
("gear",
Gear(x="x",
y="y",
module=0.1,
teeth=8,
angle=0,
shaft_size=0.02,
fill_color="#FDF6E3",
line_color="#D95F02")),
("image_url",
ImageURL(
d['x1'].append(_layout[v][0])
d['y1'].append(_layout[v][1])
d['cx0'].append(_layout[u][0] - 0.2)
d['cy0'].append(_layout[u][1] - 0.2)
d['cx1'].append(_layout[v][0] + 0.2)
d['cy1'].append(_layout[v][1] + 0.2)
return d
lines_source = ColumnDataSource(get_edges_specs(G, pos))
glyph = Bezier(x0='x0',
y0='y0',
x1='x1',
y1='y1',
cx0='cx0',
cy0='cy0',
cx1='cx1',
cy1='cy1',
line_color="#d95f02",
line_width=.5)
plot.add_glyph(lines_source, glyph)
# print(get_edges_specs(G, pos))
# r_lines = plot.multi_line('xs', 'ys', line_width=.5,
# color='grey',source=lines_source) # This function sets the color of the edges
plot.add_layout(labels)
output_file("interactive_graphs.html")
show(plot)
# write_dot(G, 'multi.dot')
def plantTree(
nameList,
parentList,
muList,
weightList,
descList,
xNodeSpread=.775,
lineMaxWidth=8, #.675
linePullFactor=0.5,
lineStartDist=0.1):
if None not in parentList:
nameList.insert(0, 'Precursor')
parentList.insert(0, None)
weightList.insert(0, 0)
descList.insert(0, [])
muList.insert(0, 0)
#maxWeight = max(weightList)
#weightList = [x/maxWeight for x in weightList]
dataTable = list(
zip(*[nameList, parentList, muList, weightList, descList]))
nameDict = {}
parentDict = {}
for index, node in enumerate(dataTable):
if node[0] not in nameDict:
nameDict[node[0]] = [node[1]]
else:
print 'ERROR Node specified twice: ' + node[0]
exit()
if node[1] not in parentDict:
parentDict[node[1]] = []
parentDict[node[1]].append(node[0])
byHeightList = []
def makeTree(curChild, curDepth):
#byHeightList
while len(byHeightList) <= curDepth:
byHeightList.append([])
byHeightList[curDepth].append(curChild)
if curChild in parentDict:
for child in parentDict[curChild]:
makeTree(child, curDepth + 1)
makeTree(None, 0)
byHeightList.pop(0)
maxWidth = max([len(x) for x in byHeightList])
#print 'Maximum amount of nodes on a single line:',maxWidth
xList = []
yList = []
nList = []
dList = []
wList = []
mList = []
for height, nodes in enumerate(byHeightList):
heightWidth = len(nodes)
for horz, node in enumerate(nodes):
#print height,horz,node,heightWidth
xList.append((horz - heightWidth / 2.) * xNodeSpread)
yList.append(height)
nList.append(node)
dList.append(descList[nameList.index(node)])
wList.append(weightList[nameList.index(node)])
mList.append(muList[nameList.index(node)])
yMax = max(yList)
yList = [yMax - y for y in yList]
hover = HoverTool(
tooltips=[("Name",
"@name"), ("Events",
"@desc"), ("Distance to parent",
"@weight"), ("Tumor fraction",
"@mu")])
plotSize = max(max(xList), len(byHeightList))
mins = plotSize / 2
maxes = plotSize / 2
print mins, maxes
margin = 1
treePlot = figure(plot_width=800,
plot_height=800,
x_range=Range1d(-plotSize * .5 - margin,
plotSize * .5 + margin),
y_range=Range1d(-.5 - margin, -.5 + plotSize + margin),
x_axis_location=None,
y_axis_location=None,
min_border=64,
v_symmetry=True,
h_symmetry=True,
active_scroll='wheel_zoom',
tools=['pan', 'wheel_zoom', 'tap', 'save', hover])
treePlot.xgrid.grid_line_color = None
treePlot.ygrid.grid_line_color = None
for parent in parentDict:
if parent not in nList:
continue
parentIndex = nList.index(parent)
fromX = xList[parentIndex]
fromY = yList[parentIndex]
for child in parentDict[parent]:
childIndex = nList.index(child)
toX = xList[childIndex]
toY = yList[childIndex]
maxD = max(len(x) for x in dList)
dWidth = len(dList[childIndex]) / float(maxD) * lineMaxWidth + 1
oldIndex = nameList.index(child)
childWeight = weightList[oldIndex]
anglePull = linePullFactor
startDist = lineStartDist
bezGlyph = Bezier(
x0=fromX,
y0=fromY - startDist,
x1=toX,
y1=toY + startDist,
cx0=fromX,
cy0=fromY - anglePull,
cx1=toX,
cy1=toY + anglePull,
line_color='black',
line_width=dWidth, #childWeight*lineMaxWidth,
line_alpha=1 - childWeight * .75)
treePlot.add_glyph(bezGlyph)
source = ColumnDataSource(data=dict(
x=xList, y=yList, desc=dList, name=nList, weight=wList, mu=mList))
renderer = treePlot.circle('x',
'y',
source=source,
color=colors[1],
line_color='#000000',
line_width=2,
radius=0.35) #0.25
selected_circle = Circle(line_width=2,
fill_color=colors[4],
line_color='#000000',
fill_alpha=1)
nonselected_circle = Circle(line_width=2,
fill_color=colors[2],
line_color='#000000',
fill_alpha=1)
renderer.selection_glyph = selected_circle
renderer.nonselection_glyph = nonselected_circle
labels = LabelSet(x='x',
y='y',
text='name',
text_align='center',
text_font_size='10px',
text_baseline='middle',
text_alpha=0.9,
x_offset=0,
y_offset=0,
source=source)
treePlot.add_layout(labels)
return treePlot
def draw_arrow_w_text_middle(scene: Plot, start: tuple, point1: tuple,
point2: tuple, end: tuple, height: int,
arrowsize: int, is_curved: bool, text: str,
font_size: int, font_family: str, over: bool,
color: tuple):
"""
# Store the appropriate function ouside of the loop
if is_curved:
shape = [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]
else:
shape = [Path.MOVETO, Path.LINETO, Path.LINETO, Path.LINETO]
# This should work, but matplotlib is not ready yet: FancyArrowPatch(path=Path([start, point1, point2, end],
s hape)
scene.add_patch(PathPatch(Path([start, point1, point2, end], shape),
edgecolor='#{0:02x}{1:02x}{2:02x}'.format(*color),
facecolor=(1, 1, 1, 0), # Transparent...
linewidth=1)) # TODO Line width!
"""
if is_curved: # cubic Bezier curve
glyph = Bezier(x0=start[0],
y0=start[1],
x1=end[0],
y1=end[1],
cx0=point1[0],
line_color='#{0:02x}{1:02x}{2:02x}'.format(*color),
cy0=point1[1],
cx1=point2[0],
cy1=point2[1],
line_width=1)
scene.add_glyph(glyph)
else:
source = ColumnDataSource(
dict(x=[start[0], end[0]], y=[start[1], end[1]]))
glyph = Line(x="x",
y="y",
line_width=1,
line_color='#{0:02x}{1:02x}{2:02x}'.format(*color))
scene.add_glyph(source, glyph)
# Draw arrow
scene.line([end[0] - arrowsize, end[0], end[0] + arrowsize],
[end[1] - arrowsize, end[1], end[1] - arrowsize],
line_color='#{0:02x}{1:02x}{2:02x}'.format(*color))
direction = 1
if over:
direction = -1
# Write label in the middle under
labelx = min(start[0], point2[0]) + abs(start[0] - point2[0]) // 2
labely = height + direction * font_size # TODO: Should be font height!
source = ColumnDataSource(dict(x=[labelx], y=[labely], text=[text]))
glyph = Text(x="x",
y="y",
text="text",
text_align="center",
text_color='#{0:02x}{1:02x}{2:02x}'.format(*color),
text_font_size=str(font_size) + "pt",
text_font=font_family)
# TODO: Here was TextToken (must align to left)
scene.add_glyph(source, glyph)
