def altitude_profile(data):
plot = Plot(title="%s - Altitude Profile" % title, plot_width=800, plot_height=400)
plot.x_range = DataRange1d()
plot.y_range = DataRange1d()
xaxis = LinearAxis(axis_label="Distance (km)")
plot.add_layout(xaxis, 'below')
yaxis = LinearAxis(axis_label="Altitude (m)")
plot.add_layout(yaxis, 'left')
xgrid = Grid(plot=plot, dimension=0, ticker=xaxis.ticker)
ygrid = Grid(plot=plot, dimension=1, ticker=yaxis.ticker)
plot.renderers.extend([xgrid, ygrid])
plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
X, Y = data.dist, data.alt
y0 = min(Y)
patches_source = ColumnDataSource(dict(
xs=[[X[i], X[i+1], X[i+1], X[i]] for i in range(len(X[:-1])) ],
ys=[[y0, y0, Y[i+1], Y[i]] for i in range(len(Y[:-1])) ],
color=data.colors[:-1]
))
patches = Patches(xs="xs", ys="ys", fill_color="color", line_color="color")
plot.add_glyph(patches_source, patches)
line_source = ColumnDataSource(dict(x=data.dist, y=data.alt))
line = Line(x='x', y='y', line_color="black", line_width=1)
plot.add_glyph(line_source, line)
return plot
def altitude_profile(data):
plot = Plot(title="%s - Altitude Profile" % title,
plot_width=800,
plot_height=400)
plot.x_range = DataRange1d()
plot.y_range = DataRange1d(range_padding=0)
xaxis = LinearAxis(axis_label="Distance (km)")
plot.add_layout(xaxis, 'below')
yaxis = LinearAxis(axis_label="Altitude (m)")
plot.add_layout(yaxis, 'left')
plot.add_layout(Grid(dimension=0, ticker=xaxis.ticker)) # x grid
plot.add_layout(Grid(dimension=1, ticker=yaxis.ticker)) # y grid
plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
X, Y = data.dist, data.alt
y0 = min(Y)
patches_source = ColumnDataSource(
dict(xs=[[X[i], X[i + 1], X[i + 1], X[i]] for i in range(len(X[:-1]))],
ys=[[y0, y0, Y[i + 1], Y[i]] for i in range(len(Y[:-1]))],
color=data.colors[:-1]))
patches = Patches(xs="xs", ys="ys", fill_color="color", line_color="color")
plot.add_glyph(patches_source, patches)
line_source = ColumnDataSource(dict(x=data.dist, y=data.alt))
line = Line(x='x', y='y', line_color="black", line_width=1)
plot.add_glyph(line_source, line)
return plot
def st_plot_wind_pressure(self):
"""
Plot wind pressure along the sign face.
The value may change for 45 degrees and a large aspect ratio.
"""
#Set up plot
plot = Plot()
#Graph of Drag Factors along sign
x = np.linspace(0, self.sign_w, num=50)
if self.wind.loadcase is Cases.FAT:
y = [
0.5 * 1.2 * self.wind.V_sit_beta.value**2 * self.C_dyn / 1000 *
self.C_fig for ix in x
]
else:
y = [
0.5 * 1.2 * self.wind.V_sit_beta.value**2 *
self.C_dyn * self.K_p / 1000 * self.C_pn_func(
self.sign_w, self.sign_h, self.wind.Wind_mult.height, ix)
for ix in x
]
source = ColumnDataSource(dict(x=x, y=y))
drag_factor = Line(x='x', y='y', line_color="#f46d43", line_width=3)
plot.add_glyph(source, drag_factor)
#Fille area under line
fill_under = Band(base='x',
upper='y',
source=source,
level='underlay',
fill_color='#55FF88')
plot.add_layout(fill_under)
#Plot setup
plot.add_layout(LinearAxis(), 'below')
plot.add_layout(LinearAxis(), 'left')
plot.xaxis.axis_label = "Distance along sign (m)"
plot.yaxis.axis_label = "Wind Pressure (kPa)"
plot.y_range = Range1d(0, max(y) * 1.3)
return plot
def _make_graph_plot(self):
""" Builds the graph portion of the final model.
"""
import networkx as nx
nodes = nx.nx_pydot.graphviz_layout(self._graph, prog="dot")
node_x, node_y = zip(*nodes.values())
models = [self._graph.nodes[x]["model"] for x in nodes]
node_id = list(nodes.keys())
node_source = ColumnDataSource(
{"x": node_x, "y": node_y, "index": node_id, "model": models}
)
edge_x_coords = []
edge_y_coords = []
for start_node, end_node in self._graph.edges:
edge_x_coords.extend([[nodes[start_node][0], nodes[end_node][0]]])
edge_y_coords.extend([[nodes[start_node][1], nodes[end_node][1]]])
edge_source = ColumnDataSource({"xs": edge_x_coords, "ys": edge_y_coords})
p2 = Plot(outline_line_alpha=0.0)
xinterval = max(max(node_x) - min(node_x), 200)
yinterval = max(max(node_y) - min(node_y), 200)
p2.x_range = Range1d(
start=min(node_x) - 0.15 * xinterval, end=max(node_x) + 0.15 * xinterval
)
p2.y_range = Range1d(
start=min(node_y) - 0.15 * yinterval, end=max(node_y) + 0.15 * yinterval
)
node_renderer = GlyphRenderer(
data_source=node_source,
glyph=Circle(x="x", y="y", size=15, fill_color="lightblue"),
nonselection_glyph=Circle(x="x", y="y", size=15, fill_color="lightblue"),
selection_glyph=Circle(x="x", y="y", size=15, fill_color="green"),
)
edge_renderer = GlyphRenderer(
data_source=edge_source, glyph=MultiLine(xs="xs", ys="ys")
)
node_hover_tool = HoverTool(tooltips=[("id", "@index"), ("model", "@model")])
node_hover_tool.renderers = [node_renderer]
tap_tool = TapTool()
tap_tool.renderers = [node_renderer]
labels = LabelSet(
x="x",
y="y",
text="model",
source=node_source,
text_font_size="8pt",
x_offset=-20,
y_offset=7,
)
help = Label(
x=20,
y=20,
x_units="screen",
y_units="screen",
text_font_size="8pt",
text_font_style="italic",
text="Click on a model to see its attributes",
)
p2.add_layout(help)
p2.add_layout(edge_renderer)
p2.add_layout(node_renderer)
p2.tools.extend(
[node_hover_tool, tap_tool, BoxZoomTool(), ResetTool(), PanTool()]
)
p2.renderers.append(labels)
self._node_source = node_source
self._edge_source = edge_source
return p2
def plotprotein(sequence, other_binding, dna_binding, metal_binding, active,
variant_location):
sequence = [i for i in sequence]
print(len(sequence))
sequence += [''] * (3000 - len(sequence))
print(sequence)
print(variant_location)
if variant_location > 50:
start_seq = variant_location - 50
else:
start_seq = 0
if variant_location + 50 < len(sequence):
end_seq = variant_location + 50
else:
end_seq = 3000
x_values = range(0, 3000)
#x_values = range(starting_value, value)
source1 = ColumnDataSource(
dict(x=x_values[start_seq:end_seq],
y=other_binding[start_seq:end_seq],
names=sequence[start_seq:end_seq]))
source2 = ColumnDataSource(
dict(x=x_values[start_seq:end_seq],
y=dna_binding[start_seq:end_seq],
names=sequence[start_seq:end_seq]))
source3 = ColumnDataSource(
dict(x=x_values[start_seq:end_seq],
y=metal_binding[start_seq:end_seq],
names=sequence[start_seq:end_seq]))
source4 = ColumnDataSource(
dict(x=x_values[start_seq:end_seq],
y=active[start_seq:end_seq],
names=sequence[start_seq:end_seq]))
glyph1 = Line(x="x", y="y", line_color="red", line_width=3, line_alpha=0.6)
glyph2 = Line(x="x",
y="y",
line_color="blue",
line_width=3,
line_alpha=0.6)
glyph3 = Line(x="x",
y="y",
line_color="green",
line_width=3,
line_alpha=0.6)
glyph4 = Line(x="x",
y="y",
line_color="orange",
line_width=3,
line_alpha=0.6)
plot = Plot(title=None,
plot_height=150,
plot_width=1000,
min_border=0,
toolbar_location=None)
plot.add_glyph(source1, glyph1)
plot.add_glyph(source2, glyph2)
plot.add_glyph(source3, glyph3)
plot.add_glyph(source4, glyph4)
plot.add_layout(
Span(location=variant_location, dimension='height',
line_color='black'))
xaxis = LinearAxis()
#YOUR_FONT_SIZE = 10
labels = LabelSet(x='x',
y=1,
text='names',
level='glyph',
x_offset=-1,
y_offset=5,
source=source1,
render_mode='canvas',
text_font_size='5pt')
plot.add_layout(labels)
yaxis = LinearAxis()
plot.add_layout(yaxis, 'left')
plot.yaxis.bounds = (0, 1)
plot.add_layout(Grid(dimension=0, ticker=xaxis.ticker))
plot.add_layout(Grid(dimension=1, ticker=yaxis.ticker))
plot.y_range = Range1d(-0.1, 1.5)
show(plot)
