def _hvplot_trajectory(self, traj):
line_gdf = self._make_line_df(traj)
if self.hvplot_is_geo and not traj.is_latlon and traj.crs is not None:
line_gdf = line_gdf.to_crs(epsg=4326)
if self.column and isinstance(self.column, str):
self.kwargs["c"] = dim(
self.column
) # fixes https://github.com/anitagraser/movingpandas/issues/71
if self.column and self.colormap:
try:
color = self.colormap[traj.df[self.column].max()]
except KeyError:
color = "grey"
return line_gdf.hvplot(
color=color,
geo=self.hvplot_is_geo,
tiles=self.hvplot_tiles,
label=traj.df[self.column].max(),
*self.args,
**self.kwargs
)
else:
return line_gdf.hvplot(
geo=self.hvplot_is_geo,
tiles=self.hvplot_tiles,
*self.args,
**self.kwargs
)
def draw_holoviews_graphs(graph_dict):
# use first key to determine default settings
first_key = list(graph_dict.keys())[0]
molecule, ksize, log2sketchsize = first_key
hv.extension('bokeh')
defaults = dict(width=400, height=400, padding=0.1)
hv.opts.defaults(opts.EdgePaths(**defaults), opts.Graph(**defaults),
opts.Nodes(**defaults))
kdims = [
hv.Dimension(('molecule', "molecule"), default=molecule),
hv.Dimension(('ksize', "k-mer size"), default=ksize),
hv.Dimension(('log2_num_hashes', "$\log_2$ num hashes"),
default=log2sketchsize),
]
kwargs = dict(width=800, height=800, xaxis=None, yaxis=None)
opts.defaults(opts.Nodes(**kwargs), opts.Graph(**kwargs))
kwargs = dict(node_size=10,
edge_line_width=1,
cmap='Set2',
node_color=dim("species"),
node_line_color='gray',
width=600,
height=600,
xaxis=None,
yaxis=None)
holomap = hv.HoloMap(graph_dict, kdims=kdims)
holomap.opts(opts.Graph(**kwargs))
return holomap
def __size_legend(size_min, size_max, dot_min, dot_max,
size_tick_labels_format, size_ticks):
size_ticks_pixels = np.interp(size_ticks, (size_min, size_max),
(dot_min, dot_max))
size_tick_labels = [size_tick_labels_format.format(x) for x in size_ticks]
points = hv.Points(
{
'x': np.repeat(0.15, len(size_ticks)),
'y': np.arange(len(size_ticks), 0, -1),
'size': size_ticks_pixels
},
vdims='size').opts(xaxis=None,
color='black',
yaxis=None,
size=dim('size'))
labels = hv.Labels(
{
'x': np.repeat(0.3, len(size_ticks)),
'y': np.arange(len(size_ticks), 0, -1),
'text': size_tick_labels
}, ['x', 'y'], 'text').opts(text_align='left', text_font_size='9pt')
overlay = (points * labels)
overlay.opts(width=dot_max + 100,
height=int(len(size_ticks) * (dot_max + 12)),
xlim=(0, 1),
ylim=(0, len(size_ticks) + 1),
invert_yaxis=True,
shared_axes=False,
show_frame=False)
return overlay
def make_plot(weight_field):
return edges_plot.opts(clone = True, node_color = "type", node_line_width=0, node_size = hv.dim("type").categorize(node_type_size_dict),
node_cmap="Category10_r",
edge_color=weight_field,edge_alpha=.9,
edge_line_width = 1.5*hv.dim(weight_field).norm()+.3,
edge_cmap="Reds", xaxis=None, yaxis=None, width=1000, height=800,
colorbar=True, inspection_policy="edges" ,bgcolor="#282829")*labels
def create_figure(x, y, color, size):
opts = dict(cmap='rainbow', width=800, height=600, line_color='black')
if color != 'None':
opts['color'] = color
if size != 'None':
opts['size'] = hv.dim(size).norm()*20
return hv.Points(df, [x, y], label="%s vs %s" % (x.title(), y.title())).opts(**opts)
def modify_doc(doc, mytabs):
start, end = 1, 20
samples_count = 5
slider = Slider(start=start, end=end, value=start, step=1, title="Counts")
select = Select(title="Count", value="aux", options=["box", "pack", "image", "user"])
renderer = hv.renderer('bokeh')##.instance(mode='server')
hv.extension('bokeh')
hv.output(size=200)
links = pd.DataFrame(data['links'])
print(links.head(3))
nodes = hv.Dataset(pd.DataFrame(data['nodes']), 'index')
chord = hv.Chord((links, nodes)).select(value=(samples_count, None))
chord.opts(opts.Chord(cmap='Category20', edge_cmap='Category20', edge_color=dim('source').str(), labels='name', node_color=dim('index').str()))
# Create HoloViews plot and attach the document
hvplot = renderer.get_plot(chord, doc)
def slider_update(attrname, old, new):
# Notify the HoloViews stream of the slider update
print ("update received")
samples_count = new
links = pd.DataFrame(data['links'])
print(links.head(3))
nodes = hv.Dataset(pd.DataFrame(data['nodes']), 'index')
chord = hv.Chord((links, nodes)).select(value=(samples_count, None))
chord.opts(opts.Chord(cmap='Category20', edge_cmap='Category20', edge_color=dim('source').str(), labels='name', node_color=dim('index').str()))
# Create HoloViews plot and attach the document
hvplot = renderer.get_plot(chord, doc)
tab3 = Panel(child=row(slider, hvplot.state), title="Chord Plot")
mytabs.append(tab3)
views = Tabs(tabs = mytabs)
layout=row(views)
doc.add_root(layout)
return doc
slider.on_change('value', slider_update)
def select_update(attrname, old, new):
# Notify the HoloViews stream of the slider update
print ("update received. Old: {} New: {}".format(old, new))
select.on_change('value', select_update)
# Combine the holoviews plot and widgets in a layout
tab3 = Panel(child=row(slider, hvplot.state), title="Chord Plot")
mytabs.append(tab3)
views = Tabs(tabs = mytabs)
layout=row(views)
doc.add_root(layout)
return doc
def chord(data):
hv.extension('bokeh')
renderer = hv.renderer('bokeh')
hv.output(size=230)
links = pd.DataFrame(data['links'])
hv.Chord(links)
nodes = hv.Dataset(pd.DataFrame(data['nodes']), 'index')
chord = hv.Chord((links, nodes)).select(value=(10, None))
chord.opts(
opts.Chord(cmap='Category20',
edge_cmap='Category20',
edge_color=dim('source').str(),
labels='name',
node_color=dim('index').str()))
bokeh_plot = renderer.get_plot(chord).state
html = file_html(bokeh_plot, CDN, "my plot")
return html
def hvplot(self, ptype="shape"):
"""
Plots the shape (Notices, it requries holoviews)
Parameters
----------
:param ptype str: Plot type. The following are excepted:
"shape": Plots the shape-edges with equal aspect-ratio
"vectors": Plots shape-edges, as well as panel-centers and tangential and normal vectors.
"""
try:
import holoviews as hv
except ImportError:
raise ImportError(
"To use the plot method holoviews is requried, see more here: http://holoviews.org/"
)
if ptype == "shape":
# Shape of airfoil (edges)
return hv.Curve(self.xy).opts(aspect='equal',
width=1000,
height=500,
padding=0.1)
elif ptype == "vectors":
# Vectors at panel centeres
pc = hv.Scatter(np.array([self.px, self.py]).T,
kdims="px",
vdims="py").opts(size=5)
vf = hv.VectorField(np.array(
[self.px, self.py,
np.angle(self.tan),
np.abs(self.tan)]).T,
label="Tangent")
vf.opts(rescale_lengths=False,
magnitude=hv.dim('Magnitude') * 0.01 * self.scale,
pivot="tail")
vfnor = hv.VectorField(np.array(
[self.px, self.py,
np.angle(self.nor),
np.abs(self.nor)]).T,
label="Normal")
vfnor.opts(rescale_lengths=False,
magnitude=hv.dim('Magnitude') * 0.01 * self.scale,
pivot="tail",
color="red") # , label="Normal")
return self.plot("shape") * pc * vf * vfnor
def _plot(self, *args, **kwargs):
@pn.depends()
def get_ax():
from matplotlib.backends.backend_agg import FigureCanvas
from matplotlib.pyplot import Figure
Interactive._fig = fig = Figure()
FigureCanvas(fig)
return fig.subplots()
kwargs['ax'] = get_ax
transform = hv.dim(self._transform, 'plot', accessor=True)
return self._clone(transform(*args, **kwargs), plot=True)
def test_pandas_transform(self):
demo_df = pd.DataFrame({
'value': np.random.randn(50),
'probability': np.random.rand(50)
})
percent = hv.dim('probability') * 100
scatter = demo_df.hvplot.scatter(x='value',
y='probability',
transforms=dict(probability=percent))
self.assertEqual((scatter.data['probability']).values,
demo_df['probability'].values * 100)
def plot_hits(self, data):
"""
This function controls evolution of hits on detector geometry. Color represents the time of hit and
the size of circle represents the size of signal on antennae. But the size of circle and
the strength of electric field/voltage on antennae are not directly related.
Hits to be plotted are binned in time so that hits are evolved in a reasonable speed.
Note that the provided antennae information (x,y,t) are already sorted based by time of hit.
'data' is sent here from 'animate' function inside a while loop.
"""
x = data[0] # updated x-coordinate of hit tanks to be plotted.
y = data[1] # updated y-coordinate of hit tanks to be plotted.
t = data[2] # updated hit time of hit tanks to be plotted.
wt = data[3] # updated weight of hit tanks to be plotted.
color = data[4] # updated colors to represent time of hit.
kdims = ['X', 'Y']
vdims = ['Weight', 'Time', 'Color']
if len(
x
) == 0: # if empty data is sent, this prevents code to fail and plots empty hits.
fig = hv.Points([], kdims=kdims, vdims=vdims)
fig.opts(
opts.Points(width=main_width,
height=main_height,
tools=['hover']))
else:
pd_data = pd.DataFrame(
data={
'X': x / 1.e3, # m --> km.
'Y': y / 1.e3, # m --> km.
'Weight': wt,
'Time': t,
'Color': color
})
ds = hv.Dataset(
pd_data) # create a holoview dataset from pandas dataframe.
'''This is the part where hits are plotted. This function is called many times and number of
hits are added in each call until all hits are included.'''
fig = hv.Points(ds, kdims=kdims, vdims=vdims)
'''Add options to the plot.'''
fig.opts(
opts.Points(
width=main_width,
height=main_height,
size=np.log(dim('Weight')) *
4., # signal strenght. This is arbitrary.
marker='circle',
color='Color',
alpha=0.95,
tools=['hover']))
return fig
def plot_chord(predictions, filename):
to_use = predictions.copy()
for n, row in predictions.iterrows():
if row.MLSynergy_score < 0:
to_use.at[n, "MLSynergy_score"] = row.MLSynergy_score * -1
to_use.at[n, "Interaction"] = "Synergy"
else:
to_use.at[n, "Interaction"] = "Antagony"
hv.extension('bokeh')
hv.output(size=200)
to_use2 = to_use[to_use.NumbDrugs == 2]
links = to_use2[["Drug1", "Drug2", "MLSynergy_score", "Interaction"]]
drugs = list(links["Drug1"].unique()) + list(links["Drug2"].unique())
nodes = hv.Dataset(drugs, 'Drug')
chord = hv.Chord((links, nodes)).select(value=(1, None))
chord.opts(opts.Chord(cmap='Rainbow', edge_cmap='Rainbow',\
edge_color=dim('Interaction').str(), labels='Drug',\
node_color=dim('Drug').str()))
output_file(filename)
show(hv.render(chord))
return to_use2
def __init__(self, data=None, **params):
data_params = {} if data is None else {k:v for k,v in data.items()
if k not in self._columns}
params = dict(data_params, **params)
data = {k:[] for k in self._columns} if (data is None) else data
super().__init__(**params)
def install_handle(plot, element):
"Handle needed to make the draw_tool available in the JS callback"
plot.handles['draw_tool'] = plot.state.tools[-1]
node_style = dict(self.node_style,
tools=['tap'],
color=hv.dim('polarity'),
fill_alpha=hv.dim('polarity').categorize({'0':0, '+':1, '-':1 }),
show_legend=False, hooks=[install_handle])
# PointDraw Stream that enables the PointDraw Bokeh tool
self._node_stream = hv.streams.PointDraw(data=data,
num_objects=self.max_nodes,
empty_value = '+')
# Nodes is a DynamicMap returning hv.Points along the boundary
self.nodes = hv.DynamicMap(self.points,
streams=[self._node_stream,
self.param.insert_points,
self.param.node_size]).opts(**node_style)
# DynamicMap drawing the boundary as a hv.Path element
self.boundary_dmap = hv.DynamicMap(self._boundary,
streams=[self._node_stream,
hv.streams.Selection1D()])
# DynamicMap placing the start indicator
self.start_marker = hv.DynamicMap(self._start_marker,
streams=[self._node_stream]
).opts(**self.start_indicator_style)
# Initial, empty mesh
self.qmesh = hv.QuadMesh((np.zeros((2,2)), np.zeros((2,2)), np.zeros((2,2))))
self._selected_edge_index = None
def __init__(self, obj, transform=None, plot=False, depth=0,
loc='top_left', center=False, dmap=False, inherit_kwargs={},
**kwargs):
self._obj = obj
self._method = None
if transform is None:
import xarray as xr
if isinstance(obj, xr.DataArray):
self._transform = hv.dim(obj.name)
else:
self._transform = hv.dim('*')
else:
self._transform = transform
self._plot = plot
self._depth = depth
self._loc = loc
self._center = center
self._dmap = dmap
self._inherit_kwargs = inherit_kwargs
self._kwargs = kwargs
ds = hv.Dataset(self._obj)
self._current = self._transform.apply(ds, keep_index=True, compute=False)
def test_xarray_transform(self):
import xarray as xr
data = np.arange(0, 60).reshape(6, 10)
x = np.arange(10)
y = np.arange(6)
da = xr.DataArray(data,
coords={
'y': y,
'x': x
},
dims=('y', 'x'),
name='value')
img = da.hvplot.image(transforms=dict(value=hv.dim('value') * 10))
self.assertEqual(img.data.value.data, da.data * 10)
def node_tab(filename):
G = scripts.MakeNetworkxGraph.__makegraph__(sep_type='semicolon',
nodes_df_link=filename)
""" Make HV network """
hv_graph = hv.Graph.from_networkx(G, nx.spring_layout,
k=1).relabel('Force-Directed Spring')
hv_graph.opts(width=650,
height=650,
xaxis=None,
yaxis=None,
padding=0.1,
node_size=hv.dim('size'),
node_color=hv.dim('node_type'),
cmap='YlOrBr',
edge_color=hv.dim('weight'),
edge_cmap='YlGnBu',
edge_line_width=hv.dim('weight'))
# Output files to Flask
renderer = hv.renderer('bokeh')
plot = renderer.get_plot(hv_graph, show=True).state
return plot
def bokeh_fig(year):
df = gapminder.query("year == %d" % (year or 1952))
return json_item(
hv.render(
hv.Points(df,
kdims=["gdpPercap",
"lifeExp"]).opts(color="continent",
size=hv.dim("pop")**(0.5) / 800,
logx=True,
height=330,
width=530,
cmap="Category10",
tools=["hover"],
legend_position="bottom_right",
title="HoloViews / Bokeh")))
def __init__(self, path, ping_file_path, speed_test_file_path):
self.path = path
self.ping_file_path = ping_file_path
self.speed_test_file_name = speed_test_file_path
# Define default layout of graphs
hv.extension('bokeh')
opts.defaults(
opts.Bars(xrotation=45, tools=['hover']),
opts.BoxWhisker(width=700, xrotation=30, box_fill_color=Palette('Category20')),
opts.Curve(width=700, tools=['hover']),
opts.GridSpace(shared_yaxis=True),
opts.Scatter(width=700, height=500, color=Palette('Category20'), size=dim('growth')+5, tools=['hover'],alpha=0.5, cmap='Set1'),
opts.NdOverlay(legend_position='left'))
if os.path.isdir(os.path.join(self.path, "webpage","figures")) is False:
os.mkdir(os.path.join(self.path, "webpage","figures"))
print("Path 'figures' created successfully")
else:
print("Path 'figures' initialized")
# Load basic configurations
config = configparser.ConfigParser()
try:
config.read('./modules/config_a.ini')
# Get values from configuration file
self.upper_acceptable_ping_bound = float(config['DEFAULT']['upper_acceptable_ping_bound'])
self.upper_ping_issue_bound = float(config['DEFAULT']['upper_ping_issue_bound'])
self.acceptable_network_speed = float(config['DEFAULT']['acceptable_network_speed'])
except:
# In case no config-file is found or another reading error occured
print("Configuration file not found/readable.")
print("Creating a new configuration file.")
# Creating new file with standard values
config['DEFAULT'] = {'upper_acceptable_ping_bound': '10',
'upper_ping_issue_bound': '99999',
'acceptable_network_speed': '16'}
with open('config_a.ini', 'w') as configfile:
config.write(configfile)
print("New configuration file was created. Running on default parameters, please restart for changes.")
#set default values to continue with program
self.upper_acceptable_ping_bound = float(config['DEFAULT']['upper_acceptable_ping_bound'])
self.upper_ping_issue_bound = float(config['DEFAULT']['upper_ping_issue_bound'])
self.acceptable_network_speed = float(config['DEFAULT']['acceptable_network_speed'])
def __getattr__(self, name):
if name in dir(self):
if self._method:
transform = hv.dim(self._transform, self._method, accessor=True)
inherit_kwargs = {}
if self._method == 'plot':
inherit_kwargs['ax'] = self._get_ax_fn()
new = self._clone(transform, inherit_kwargs=inherit_kwargs)
else:
new = self
new._method = name
try:
new.__doc__ = getattr(new, name).__doc__
except Exception:
pass
return new
raise AttributeError(name)
def create_artists_points(data):
artists_tooltips = """
<div>
<div>
<img
src="@image" height="70" alt="@image" width="70"
style="float: left; margin: 0px 15px 15px 0px;"
border="1"
></img>
</div>
<div>
<span style="font-size: 15px;"><b>@name</b></span>
</div>
<div>
<span style="font-weight: bold;">Main genre:</span>
<span>@genre_cluster</span>
</div>
<div>
<span style="font-weight: bold;">Subgenre:</span>
<span>@genre_specific</span>
</div>
</div>
"""
artists_hover = HoverTool(tooltips=artists_tooltips)
artists_points = hv.Points(data=data,
kdims=["genre_x", "genre_y"],
vdims=[
"genre_cluster", "genre_specific",
"popularity", "image", "name"
])
artists_points.opts(
tools=["box_select", "lasso_select", artists_hover, "tap"],
color="genre_cluster",
cmap="dark2",
line_color="black",
size=hv.dim("popularity") / 5,
padding=0.1,
width=800,
height=600,
show_grid=False,
show_frame=False,
xaxis="bare",
yaxis="bare",
title="Artists")
return artists_points
def generateGraph(choice):
value_dim = hv.Dimension('Percentage', unit='%')
if choice == 'Feelings about Future':
sankey = hv.Sankey((fearEdges,fearNodes), ['From','To'], vdims=value_dim)
#sankey = hv.Sankey([(fearTable[i],fearTable[j],k) for i,j,k in fearEdges], ['From','To'], vdims=value_dim)
sankey.opts(title='How Tech Savviness Influences Feelings about Connectivity')
elif choice == 'Importance Rankings':
sankey = hv.Sankey((rankEdges,rankNodes), ['From','To'], vdims=value_dim)
#sankey = hv.Sankey([(rankTable[i],rankTable[j],k) for i,j,k in rankEdges], ['From','To'], vdims=value_dim)
sankey.opts(title='How Tech Savviness Influences Priorities when Purchasing New Devices')
sankey.opts(labels='label',
width=1000,
height=900,
cmap=jankyCmap,
edge_color=dim('From').str(),
fontsize={'title': 18, 'labels': 16},
node_hover_fill_color='grey',
tools=[hover])
return sankey
def ChordDiagram(self):
# Step 1 Get Data
self.sharedNeos = self.GetShared()
self.matchedNeos = self.GetMatchedNeos()
hv.output(size=200)
source = []
target = []
value = []
for i, sam in enumerate(self.sharedNeos):
for pair in self.sharedNeos[sam]:
source.append(sam + "_" + pair.split(',')[0])
target.append(sam + "_" + pair.split(',')[1])
value.append(self.sharedNeos[sam][pair])
for matched in self.matchedNeos:
source.append(matched.split(',')[0])
target.append(matched.split(',')[1])
value.append(self.matchedNeos[matched])
links = pd.DataFrame({
'source': source,
'target': target,
'value': value
})
chord = hv.Chord(links)
# chord = hv.Chord((links, nodes)).select(value=(5, None))
chord.opts(
opts.Chord(cmap='Category20',
edge_cmap='Category20',
labels='index',
node_color=dim('index').str()))
p = hv.render(chord)
select = Select(title="Option:",
value="foo",
options=["foo", "bar", "baz", "quux"])
return (p, select)
def plot_player_ratings_scatter(
player_ratings: pd.DataFrame,
x_col: str,
y_col: str,
color_col: str = "overall",
size_col: str = "overall",
**plot_opts,
) -> hv.Overlay:
scatter_base = (player_ratings.reset_index().hvplot.scatter(
x=x_col,
y=y_col,
c=color_col,
hover_cols=["name", "overall"],
).opts(
size=abs(dim(size_col)) * 2,
**plot_opts,
))
overlay = (scatter_base * hv.VLine(0).opts(color="gray") *
hv.HLine(0).opts(color="gray"))
return overlay
def slider_update(attrname, old, new):
# Notify the HoloViews stream of the slider update
print ("update received")
samples_count = new
links = pd.DataFrame(data['links'])
print(links.head(3))
nodes = hv.Dataset(pd.DataFrame(data['nodes']), 'index')
chord = hv.Chord((links, nodes)).select(value=(samples_count, None))
chord.opts(opts.Chord(cmap='Category20', edge_cmap='Category20', edge_color=dim('source').str(), labels='name', node_color=dim('index').str()))
# Create HoloViews plot and attach the document
hvplot = renderer.get_plot(chord, doc)
tab3 = Panel(child=row(slider, hvplot.state), title="Chord Plot")
mytabs.append(tab3)
views = Tabs(tabs = mytabs)
layout=row(views)
doc.add_root(layout)
return doc
def era5_static(era5_data, hour, wind):
"""
Static wind vectorfield at specific hour and height (10/100m)
"""
if wind == 10:
angle = 'rad_10'
mag = 'intensity_10'
else:
angle = 'rad_100'
mag = 'intensity_100'
return (era5_data.sel(Time=str(im[0][0].value) +
'T{hour:02d}'.format(hour=hour)).hvplot.vectorfield(
x='lon',
y='lat',
angle=angle,
mag=mag,
hover=False)).opts(magnitude=dim(mag) * 0.01,
color=mag,
colorbar=True,
rescale_lengths=False,
ylabel='latitude')
def _hvplot_trajectory(self, traj):
line_gdf = self._make_line_df(traj)
if not traj.is_latlon and traj.crs is not None:
line_gdf = line_gdf.to_crs(epsg=4326)
if self.column and type(self.column) == str:
self.kwargs['c'] = dim(
self.column
) # fixes https://github.com/anitagraser/movingpandas/issues/71
if self.column and self.column_to_color:
try:
color = self.column_to_color[traj.df[self.column].max()]
except KeyError:
color = 'grey'
return line_gdf.hvplot(color=color,
geo=self.hvplot_is_geo,
tiles=self.hvplot_tiles,
*self.args,
**self.kwargs)
else:
return line_gdf.hvplot(geo=self.hvplot_is_geo,
tiles=self.hvplot_tiles,
*self.args,
**self.kwargs)
def chord_diagram(self, launch):
try:
def normalize_value(x, total):
x = int((x / total) * 1000)
if x <= 0:
return 1
return x
df = self.df.copy()
# -------------- nodes
data = {}
data['nodes'] = []
source_list = df['milestone_owner'].tolist()
names = list(set(source_list))
person_type_dict = dict(zip(df.milestone_owner, df.type))
type_dict = {}
types = list(set(df['type'].tolist()))
name_dict = {}
for idx, name in enumerate(names):
name_dict[name] = idx
for idx, name in enumerate(names):
type_tmp = person_type_dict[name]
index = name_dict[name]
data['nodes'].append({
'OwnerID': index,
'index': idx,
'Type': type_tmp
})
nodes = hv.Dataset(pd.DataFrame(data['nodes']), 'index')
# --------- make the links
data['links'] = []
for idx, row in df.iterrows():
src = name_dict[row['project_owner']]
tgt = name_dict[row['milestone_owner']]
val = row['remuneration']
data['links'].append({
'source': src,
'target': tgt,
'value': val
})
links = pd.DataFrame(data['links'])
# get the individual links
links = links.groupby(['source', 'target'])['value'].sum()
links = links.reset_index()
total = links['value'].sum()
links['value'] = links['value'].apply(
lambda x: normalize_value(x, total))
# filter for top percentile
quantile_val = links['value'].quantile(
self.chord_data['percentile_threshold'])
links = links[links['value'] >= quantile_val]
#logger.warning('after quantile filter:%s',len(links))
chord_ = hv.Chord((links, nodes), ['source', 'target'],
['value'])
chord_.opts(
opts.Chord(cmap='Category20',
edge_cmap='Category20',
edge_color=dim('source').str(),
labels='Type',
node_color=dim('index').str(),
width=1000,
height=1000))
return chord_
except Exception:
logger.error('chord diagram', exc_info=True)
# Specify the plot render to use
hv.extension('bokeh')
hv.output(size=300)
# Chord diagram with interactive components
edgeList = edges[['Source', 'Target', 'weight']]
# Within the holoviews dataset object we define kdim and vdims
# Kdims are the independent variables which is Id in this example
# Vdims are dependent variables cent_value and rank_value
# By defining these here were can use them when creating the graph
nodeDS = hv.Dataset(nodes_extended, 'Id', ['cent_value', 'rank_value'])
# Coloured interactive chord diagram with node size determined by Vdims
kwargs = dict(width=300, height=300, xaxis=None, yaxis=None)
opts.defaults(opts.Nodes(**kwargs), opts.Graph(**kwargs))
graph = hv.Graph((edgeList, nodeDS), label='GoT season 1')
graph.opts(cmap='Category20',
edge_cmap='Category20',
node_size='cent_value',
edge_line_width=1,
node_color=dim('Id').str(),
edge_color=dim('Source').str())
graph.opts(
opts.Chord(inspection_policy='nodes',
tools=['hover'],
edge_hover_line_color='green',
node_hover_fill_color='red'))
hv.save(graph, 'node_size_chord.html')
#plot = figure(title="Networkx Integration Demonstration", x_range=(-1.1,1.1), y_range=(-1.1,1.1),
#tools="", toolbar_location=None)
#graph = hv.Graph.from_networkx(B, nx.bipartite_layout(B, nodes=l)).opts(tools=['hover'], directed=True,
# node_size=25, inspection_policy='edges',
#arrowhead_length=0.1)
# , vdims='weight')
#plot.hv.render(graph)
#output_file("networkx_graph.html")
#show(plot)
renderer = hv.renderer('bokeh')
# actually drawing the graph with holoviews
flowchart = hv.Graph.from_networkx(B, nx.bipartite_layout(B, nodes=l), vdims='weight').opts(tools=['hover'], directed=True,
node_size=25, inspection_policy='edges',
arrowhead_length=0.1)
#edge_line_width=B.nodes('weight'))
#, vdims='weight')
labels = hv.Labels(flowchart.nodes, ['x', 'y'], 'index')
#layout = flowchart * labels.opts(text_font_size='8pt', text_color='red', bgcolor='white')
#doc = renderer.server_doc(layout)
show(hv.render(flowchart.opts(edge_line_width=hv.dim('weight')*3) * labels.opts(text_font_size='8pt', text_color='red',
bgcolor='white')))
#from bokeh.server.server import Server
#server = Server({'/': app}, port=0)
# Set up StreamingDataFrame and add async callback
cpu_stream = hv.streams.Buffer(get_cpu_data(), 800, index=False)
mem_stream = hv.streams.Buffer(get_mem_data())
def cb():
cpu_stream.send(get_cpu_data())
mem_stream.send(get_mem_data())
# Define DynamicMaps and display plot
cpu_dmap = hv.DynamicMap(cpu_box, streams=[cpu_stream])
mem_dmap = hv.DynamicMap(mem_stack, streams=[mem_stream])
plot = (cpu_dmap + mem_dmap).opts(
opts.Area(height=400, width=400, ylim=(0, 100)),
opts.BoxWhisker(box_fill_color=dim('CPU').str(),
cmap='Category20',
width=500,
height=400,
ylim=(0, 100)))
# Render plot and attach periodic callback
doc = renderer.server_doc(plot)
doc.add_periodic_callback(cb, 0.05)
'Life expectancy': dict(label='Life expectancy at birth (years)', range=(15, 100)),
'Population': ('population', 'Population')
}
# Create Points plotting fertility vs life expectancy indexed by Year
gapminder_ds = ds.redim(**dimensions).to(hv.Points, kdims, vdims, 'Year')
# Define annotations
text = gapminder_ds.clone({yr: hv.Text(1.2, 25, str(int(yr)), fontsize=30)
for yr in gapminder_ds.keys()})
# Define options
# Combine Points and Text
hvgapminder = (gapminder_ds * text).opts(
opts.Points(alpha=0.6, color='Group', cmap='Set1', line_color='black',
size=np.sqrt(dim('Population'))*0.005, width=1000, height=600,
tools=['hover'], title='Gapminder Demo'),
opts.Text(text_font_size='52pt', text_color='lightgray'))
# Define custom widgets
def animate_update():
year = slider.value + 1
if year > end:
year = start
slider.value = year
# Update the holoviews plot by calling update with the new year.
def slider_update(attrname, old, new):
hvplot.update((new,))
return hv.Area.stack(areas.overlay()).relabel('Memory')
def cpu_box(data):
return hv.BoxWhisker(data, 'CPU', 'Utilization').relabel('CPU Usage')
# Set up StreamingDataFrame and add async callback
cpu_stream = hv.streams.Buffer(get_cpu_data(), 800, index=False)
mem_stream = hv.streams.Buffer(get_mem_data())
def cb():
cpu_stream.send(get_cpu_data())
mem_stream.send(get_mem_data())
# Define DynamicMaps and display plot
cpu_dmap = hv.DynamicMap(cpu_box, streams=[cpu_stream])
mem_dmap = hv.DynamicMap(mem_stack, streams=[mem_stream])
plot = (cpu_dmap + mem_dmap).opts(
opts.Area(height=400, width=400, ylim=(0, 100)),
opts.BoxWhisker(box_fill_color=dim('CPU').str(), cmap='Category20',
width=500, height=400, ylim=(0, 100)))
# Render plot and attach periodic callback
doc = renderer.server_doc(plot)
doc.add_periodic_callback(cb, 0.05)
