def histogram(arr, xlbl, xrng=None, nbins=20, alpha=1.):
""" Generate a bokeh histogram
Parameters
----------
arr : ndarray
xlbl : str
Label for the x-axis
xrng : tuple, optional
xmin, xmax
nbins : int, optional
number of bins
alpha : float, optional
alpha for
"""
if xrng is None:
xrng = (np.min(arr),np.max(arr))
p = figure(plot_width=600, plot_height=400)
# Histogram
hist, edges = np.histogram(arr, range=xrng, density=True, bins=nbins)
p.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:], fill_color='blue', alpha=alpha)
# Label
p.xaxis.axis_label = xlbl
# Show
show(p)
def test_show_doesnt_duplicate_if_already_there(m):
io._state.document.clear()
p = Plot()
io.show(p)
assert io._state.document.roots == [p]
io.show(p)
assert io._state.document.roots == [p]
def df_plot(dfD, xCol, yCols, width=600, height=600):
hover1 = HoverTool(tooltips=[("x,y", "(@x, @y)")])
tools1 = ["pan,resize,box_zoom,wheel_zoom,crosshair",hover1,"reset,save"]
hover2 = HoverTool(tooltips=[("x,y", "(@x, @y)")])
tools2 = ["pan,resize,box_zoom,wheel_zoom,crosshair",hover2,"reset,save"]
plot1 = figure(width=width, height=height, tools=tools1)
plot2 = figure(width=width, height=height, tools=tools2,
x_range=plot1.x_range, y_range=plot1.y_range)
tab1 = Panel(child=plot1, title="line + points")
tab2 = Panel(child=plot2, title="points only")
for i in yCols:
if dfD.iloc[:,i].count() > 0:
plot1.line(dfD.iloc[:,xCol],dfD.iloc[:,i], line_color=colors[i], line_width=1, legend=dfD.columns[i])
plot1.scatter(dfD.iloc[:,xCol],dfD.iloc[:,i], marker="+", line_color=colors[i], line_width=1, legend=dfD.columns[i])
plot2.scatter(dfD.iloc[:,xCol],dfD.iloc[:,i], marker="+", line_color=colors[i], line_width=1, legend=dfD.columns[i])
tabs = Tabs(tabs=[ tab1, tab2 ])
show(tabs)
return tabs
def create_map(tab_del_file):
"""
This function was adapted from bokeh tutorial, so it might have similar
elements in it.
"""
data = pandas.read_csv(tab_del_file, sep="\\t", engine='python')
lat_mean = data["Lat"].mean()
long_mean = data["Long"].mean()
map_options = GMapOptions(lat=lat_mean, lng=long_mean, map_type="hybrid",
zoom=5)
plot = GMapPlot(x_range=DataRange1d(),
y_range=DataRange1d(),
map_options=map_options,
title="PopART-XTREME"
)
source = ColumnDataSource(data=dict(lat=[x for x in data["Lat"]],
lon=[y for y in data["Long"]],
name=[s for s in data["Sequence"]],
local=[l for l in data["Locality"]]))
circle = Circle(x="lon", y="lat", size=15, fill_color="blue",
fill_alpha=0.8, line_color=None)
tooltips = [("Sequence", "@name"), ("Locality", "@local")]
render = plot.add_glyph(source, circle)
plot.add_tools(PanTool(), WheelZoomTool(), BoxSelectTool(), BoxZoomTool(),
PreviewSaveTool(), HoverTool(tooltips=tooltips,
renderers=[render]))
output_file("map_plot.html")
show(plot)
def stockPlots():
# Load the index data so that it can be plotted
dateDataSP500, openDataSP500 = SP500.convertPlotData(percentage='y')
dateDataSSEC, openDataSSEC = SSEC.convertPlotData(percentage='y')
dateDataN225, openDataN225 = N225.convertPlotData(percentage='y')
dateDataASX, openDataASX = ASX.convertPlotData(percentage='y')
dateDataFTSE, openDataFTSE = FTSE.convertPlotData(percentage='y')
#Plots data using Bokeh
pTest = figure(plot_width=1200, plot_height=700, title="Stock Indices")
pTest.line(dateDataSP500, openDataSP500, line_width=2, line_color="green", legend = "S&P 500")
pTest.line(dateDataSSEC, openDataSSEC, line_width=2, line_color="red", legend="SSEC")
pTest.line(dateDataN225, openDataN225, line_width=2, legend="N225")
pTest.line(dateDataASX, openDataASX, line_width=2, line_color="orange", legend="ASX")
pTest.line(dateDataFTSE, openDataFTSE, line_width=2, line_color="purple", legend="FTSE")
pTest.xaxis.axis_label = "Date"
pTest.yaxis.axis_label = "Percentage change (%)"
pTest.legend.location = "top_left"
pTest.xaxis[0].formatter = DatetimeTickFormatter(formats = dict(hours=["%B %Y"],
days=["%B %Y"],
months=["%B %Y"],
years=["%B %Y"],))
script, div = components(pTest)
return render_template("simpleline.html", script=script, div=div)
show(pTest)
def test_zeppelin_with_notebook_handle(self):
load_zeppelin_args = (Resources(), True, True, 1000, 'zeppelin')
io.output_notebook(*load_zeppelin_args)
with pytest.raises(Exception) as ex:
p = Plot()
io.show(p, notebook_handle=True)
assert "Zeppelin doesn't support notebook_handle." == str(ex.value)
def plot_simple_bokeh_line(x,y, filename, height, width, xaxis, yaxis, title):
output_file(filename)
p=figure(plot_width=width, plot_height=height,title=title)
p.line(x,y, color="green")
p.xaxis.axis_label=xaxis
p.yaxis.axis_label=yaxis
show(p)
def correlationsBar():
# Creates a bar plot showing the fraction of years that correlations have gone
# below 0.
# Create a dictionary of the different pairs of stocks for correlations calculations
combinations = {'SP500-SSEC':[SP500,SSEC],'SP500-N225':[SP500,N225],'SP500-ASX':[SP500,ASX],
'SP500-FTSE':[SP500,FTSE],'SSEC-N225':[SSEC,N225],'SSEC-ASX':[SSEC,ASX],
'SSEC-FTSE':[SSEC,FTSE],'N225-ASX':[N225,ASX],'N225-FTSE':[N225,FTSE],'ASX-FTSE':[ASX,FTSE]}
#Calculate the fraction of years that the correlations were less than 0
fracNeg =[]
for x in combinations.keys():
fracNeg.append(negativeCorrelation(combinations[x][0],combinations[x][1]))
# Add data to dataframe for plotting
dictTest = {'values':fracNeg, 'names':combinations.keys()}
df = pd.DataFrame(dictTest)
#Plots data using Bokeh
pTest = figure(plot_width=1200, plot_height=700, title="Correlations with S&P500")
pTest = Bar(df, 'names', values='values', title = "Fraction of years where correlations are below 0",
xlabel="Indices", ylabel="Fraction of years below 0")
script, div = components(pTest)
return render_template("simpleline.html", script=script, div=div)
show(pTest)
def plot_spec_notebook(spec, title=None, xmnx=None, ymnx=None):
""" Simple spectrum plot in a Notebook
Parameters
----------
spec : XSpectrum1D
title : str, optional
xmnx : list or tuple or ndarray
xmin, xmax values
ymnx : list or tuple or ndarray
ymin, ymax values
"""
p = figure(plot_width=900, plot_height=500, title=title)
# Data
p.line(spec.dispersion.value, spec.flux.value, color='black', line_width=2)
p.line(spec.dispersion.value, spec.sig, color='red', line_width=0.5)
# Labels
p.xaxis.axis_label = "Wavelength"
p.yaxis.axis_label = "Flux"
# Axes
if xmnx is not None:
p.set(x_range=Range1d(xmnx[0], xmnx[1]))
if ymnx is not None:
p.set(y_range=Range1d(ymnx[0], ymnx[1]))
# Show
show(p)
def plot_to_bokeh(data_frame, channels_names, desired_col_index=-1):
'''
:param data_frame: pandas dataframe
:param desired_col_index: -1 for all, i>0 for any other
:return: non
'''
if desired_col_index>=0:
header_str = data_frame._info_axis.values[desired_col_index]
col_data = data_frame._series[channels_names[desired_col_index]].values # returns nd_array
# data_frame[data_frame._info_axis.values[3]]
print col_data
###################
output_file("iris.html")
# Create the figure object
f = figure()
# adding glyphs
f.circle(range(0,len(col_data)), col_data)
# Save and show the figure
show(f)
print f
###################
return col_data
def create_heatmap(station_scores, plot_width=1000, plot_height=600):
map_options = GMapOptions(lat=32.06, lng=34.87, map_type="roadmap", zoom=9)
cmap = plt.get_cmap('jet')
plot = GMapPlot(
x_range=DataRange1d(), y_range=DataRange1d(), map_options=map_options, title="Israel"
)
plot.plot_width = plot_width
plot.plot_height = plot_height
lat_vec = list(map(lambda x: get_loc_by_id(x).lat, station_scores.keys()))
lon_vec = list(map(lambda x: get_loc_by_id(x).lon, station_scores.keys()))
for ind, station in enumerate(station_scores):
source = ColumnDataSource(
data=dict(
lat=[lat_vec[ind]],
lon=[lon_vec[ind]],
)
)
cmap_indx = int(station_scores[station]*cmap.N)
cmap_val = tuple(np.floor(255 * np.array(cmap(cmap_indx)[:3])))
circle = Circle(x="lon", y="lat", size=17, fill_color=cmap_val, fill_alpha=0.95, line_color=None)
plot.add_glyph(source, circle)
plot.add_tools(PanTool(), WheelZoomTool())
output_file("Mean Time to Tel-Aviv Hashalom.html")
show(plot)
def notebook(*tunnels, mon_local=True, plot_list: Sequence = None):
"""
Output monitor to a notebook
This command will block the notebook until interrupted
:param tunnels: strings
ssh arguments used for logging into remote machines
Example:
"-p 5900 myuser@somehost" -> log in using port 5900 with "mysuser" on "somehost"
For every ssh string a monitor column will be added to the interface
:param mon_local: bool
should the local machine be monitored?
:param plot_list: Sequence of strings or None
if not None, it overrides the default plots. use methods names of
BokehPlots class
:return: None
"""
from bokeh.io import show
execs = make_tunnels(tunnels, mon_local)
plots = monitors, change_streams = generate_plots(execs)
show(plots)
loop = asyncio.get_event_loop()
loop.run_until_complete(asyncio.gather(
*(mon() for mon in monitors),
*(changes.start() for changes in change_streams)
))
def notebook(*tunnels):
from bokeh.io import show
execs = dict()
if tunnels:
for tunnel in tunnels:
t_args = re.findall('([\'"]([^"\']+)["\'])|([^ ]+)', tunnel)
t_args = [a[-1] if a[-1] else a[-1] for a in t_args]
t_args = [a.strip(' ') for a in t_args]
execs['_'.join(t_args)] = make_ssh_subprocess(*t_args)
else:
execs['localhost'] = async_subprocess, Popen
_hplots = list()
monitors = list()
change_streams = list()
for ex in execs.values():
changes = ChangeStream(source_fun=update_notebook_source)
mon = RessourceMonitor(changes, async_exec=ex[0], normal_exec=ex[1])
plot_gen = BokehPlots(changes, async_exec=ex[0], normal_exec=ex[1])
_hplots.append(vplot(plot_gen.cpu_bars(False), plot_gen.gpu_bars(),
plot_gen.user_total_memusage()))
monitors.append(mon)
change_streams.append(changes)
plots = hplot(*_hplots)
show(plots)
loop = asyncio.get_event_loop()
loop.run_until_complete(asyncio.gather(
*(mon.gpus_mon(loop=loop) for mon in monitors),
*(mon.cpus_mon() for mon in monitors),
*(changes.start() for changes in change_streams)
))
def plot_matplobli(self):
from omicexperiment.plotting.plot_bokeh import plot_interactive
fig = plot_interactive(self.data_df)
from bokeh.io import show, output_notebook
output_notebook()
show(fig)
return fig
def hist_plot(self, bokeh=False):
""" Simple histogram plot of the PDF
Parameters
----------
bokeh : bool, optional
Generate a bokeh plot?
Returns
-------
"""
if not bokeh:
from matplotlib import pyplot as plt
# imports
try:
import seaborn as sns; sns.set_style("white")
except:
pass
# Giddy up
plt.clf()
plt.bar(self.x-self.dx/2., self.pdf, width=self.dx)
plt.xlabel("x")
plt.ylabel("PDF(x)")
plt.show()
plt.close()
else:
from bokeh.io import show
from bokeh.plotting import figure
p = figure(plot_width=400, plot_height=400, title='x PDF')
p.quad(top=self.pdf, bottom=0, left=self.x-self.dx/2.,
right=self.x+self.dx/2.)
p.xaxis.axis_label = 'x'
# Show
show(p)
def make_map(self, map_type, title):
options = GMapOptions(lat=43.7, lng=-79.4, map_type=map_type, zoom=11)
plot = GMapPlot(x_range=DataRange1d(),
y_range=DataRange1d(),
map_options=options,
title=title)
output_file('plot.html')
show(plot)
def test_show_with_app(self, mock__run_notebook_hook):
app = Application()
io.show(app, notebook_url="baz")
io._state.notebook_type == "foo"
self.assertTrue(mock__run_notebook_hook.called)
self.assertEqual(mock__run_notebook_hook.call_args[0][0], io._state.notebook_type)
self.assertEqual(mock__run_notebook_hook.call_args[0][1:], ("app", app, io._state, "baz"))
self.assertEqual(mock__run_notebook_hook.call_args[1], {})
def plot_cross_variograms(self, iter_plot=200, trace=None, experimental=None):
"""
Plot the analytical cross-variogram of a given MCMC inference
Args:
iter_plot (int): Number of traces to plot
trace (pymc3.trace): trace with the sill, range and weights of each property
experimental (bool): if True plot the experimental variogram as well
Returns:
None
"""
if not trace:
trace = self.trace
assert trace, 'set the trace to the object'
n_exp = self.n_exp
n_gauss = self.n_gauss
lags = self.lags
# DEP- n_equations = trace['weights'].shape[1]
n_iter = trace['weights'].shape[0]
lags_tiled = np.tile(lags, (iter_plot, 1))
b_var = []
for i in range(0, self.n_properties): # DEP- n_equations, (n_exp+n_gaus)):
# Init tensor
b = np.zeros((len(lags), n_iter, 0))
for i_exp in range(0, n_exp):
b = np.dstack((b, trace['weights'][:, i_exp + i * (n_exp + n_gauss)] *
exp_vario(lags, trace['sill'][:, i_exp], trace['range'][:, i_exp])))
for i_gauss in range(n_exp, n_gauss + n_exp):
b = np.dstack((b, trace['weights'][:, i_gauss + i * (n_exp + n_gauss)] *
gaus_vario(lags, trace['sill'][:, i_gauss], trace['range'][:, i_gauss])))
# Sum the contributins of each function
b_all = b.sum(axis=2)
# Append each variable
b_var.append(b_all[:, -iter_plot:].T)
# Bokeh code to plot this
p_all = []
for e, el in enumerate(self.properties):
p = bp.figure()#x_axis_type="log")
p.multi_line(list(lags_tiled), list(b_var[e]), color='olive', alpha=0.08)
if experimental:
p.scatter(self.lags, y=self.exp_var[el], color='navy', size=2)
p.title.text = el
p.xaxis.axis_label = "lags"
p.yaxis.axis_label = "Semivariance"
p_all = np.append(p_all, p)
grid = bl.gridplot(list(p_all), ncols=5, plot_width=250, plot_height=150)
show(grid)
def plot_im_grid(imarray, dims):
x, y, z = dims
plot_list = []
for layer, depth in zip(range(imarray.shape[-1]), z):
p = figure(x_range=[x[0], x[-1]], y_range=[y[0], y[-1]],
title="Depth %.0f mm"%(depth))
p.image(image=[np.squeeze(imarray[:,:,layer])], x=[0], y=[0],
dw=x[-1], dh=y[-1], palette="Greys9")
plot_list.append(p)
grid = gridplot([plot_list[:6],plot_list[6:12],plot_list[12:]])
show(grid)
return components(grid)
def UpdatePlot(source, source1):
data_table.source=source1
plotClusters(source, p)
#set callbacks
#sliders[0].callback = cb.callbackMin(source)
#sliders[1].callback = cb.callbackMax(source)
#taptool.callback = cb.callbackTap(source)
curdoc().add(vbox)
#session = push_session(curdoc())
#session.show(vbox)
show(curdoc())
def plot_cross_covariance(self, nuggets=False, iter_plot=200):
"""
Plot the cross covariance for the given properties
Args:
nuggets (numpy.array): subtracted nuggets
iter_plot (int): number of traces to plot
Returns:
None
"""
n_exp = self.n_exp
n_gauss = self.n_gauss
trace = self.trace
lags = self.lags
n_equations = trace['weights'].shape[1]
n_iter = trace['weights'].shape[0]
lags_tiled = np.tile(lags, (iter_plot, 1))
b_var = []
for i in range(0, self.n_properties): # n_equations, (n_exp+n_gaus)):
# Init tensor
b = np.zeros((len(lags), n_iter, 0))
for i_exp in range(0, n_exp):
# print(i_exp, "exp")
b = np.dstack((b, trace['weights'][:, i_exp + i * (n_exp + n_gauss)] *
exp_vario(lags, trace['sill'][:, i_exp], trace['range'][:, i_exp])))
for i_gaus in range(n_exp, n_gauss + n_exp):
# print(i_gaus)
b = np.dstack((b, trace['weights'][:, i_gaus + i * (n_exp + n_gauss)] *
gaus_vario(lags, trace['sill'][:, i_gaus], trace['range'][:, i_gaus])))
# Sum the contributins of each function
if nuggets:
b_all = 1 - (b.sum(axis=2) + self.nuggets[i])
else:
b_all = 1 - (b.sum(axis=2))
# Append each variable
b_var.append(b_all[:, -iter_plot:].T)
p_all = []
for e, el in enumerate(self.properties):
p = bp.figure(x_axis_type="log")
p.multi_line(list(lags_tiled), list(b_var[e]), color='olive', alpha=0.08)
p.title.text = el
p.xaxis.axis_label = "lags"
p.yaxis.axis_label = "Semivariance"
p_all = np.append(p_all, p)
grid = bl.gridplot(list(p_all), ncols=5, plot_width=250, plot_height=150)
show(grid)
def box_plot_sim_game(df_results_team):
# values to represent
# score, two_pt_shots_attempt/made, three_pt_shots_made/attempts, off/def rebounds
rel_col = [
'PTS', 'FGA', 'FGM', 'FG3A', 'FG3M',
'OREB', 'DREB', 'STL', 'BLK', 'TO', 'PASS'
]
# get quartile info
# q4=min, q5=max
q1, q2, q3, q4, q5 = {}, {}, {}, {}, {}
for col in rel_col:
q1[col] = df_results_team[col].quantile(q=0.25)
q2[col] = df_results_team[col].quantile(q=0.50)
q3[col] = df_results_team[col].quantile(q=0.75)
q4[col] = df_results_team[col].quantile(q=0.00)
q5[col] = df_results_team[col].quantile(q=1.00)
df = pd.DataFrame([q1, q2, q3, q4, q5]).T
df.columns = ['q{}'.format(i) for i, col in enumerate(df, 1)]
iqr = df.q3 - df.q1
upper = df.q3 + 1.5 * iqr
lower = df.q1 - 1.5 * iqr
new_upper = [min([x, y]) for (x, y) in zip(df.q5.values, upper.values)]
new_lower = [max([x, y]) for (x, y) in zip(df.q4.values, lower.values)]
p = figure(tools="save", background_fill_color="#EFE8E2", title="", x_range=rel_col)
# stems
p.segment(rel_col, new_upper, rel_col, df.q3.values, line_color="black")
p.segment(rel_col, new_lower, rel_col, df.q1.values, line_color="black")
# boxes
p.vbar(rel_col, 0.7, df.q2.values, df.q3.values, fill_color='#FF1493', line_color="black")
p.vbar(rel_col, 0.7, df.q1.values, df.q2.values, fill_color='#1E90FF', line_color="black")
# whiskers (almost-0 height rects simpler than segments)
p.rect(rel_col, new_lower, 0.2, 0.01, line_color="black")
p.rect(rel_col, new_upper, 0.2, 0.01, line_color="black")
p.xgrid.grid_line_color = None
p.ygrid.grid_line_color = "white"
p.grid.grid_line_width = 2
p.xaxis.major_label_text_font_size = "12pt"
output_file("box.html")
show(p)
def plotStockData(self, percentage='n'):
# calls readDatabase, then uses pylab to plot the stock data from initialDate
# to finalDate. Defaults are minDate and maxDate.
#Read in stock data
dateData, openData = self.convertPlotData(percentage='n')
#Plots data using Bokeh
pTest = figure(plot_width=500, plot_height=500, title="Stock Indices")
pTest.line(dateData, openData, line_width=2)
pTest.xaxis.axis_label = "Date"
pTest.yaxis.axis_label = "Index Level"
show(pTest) # show the results
return pTest
def main():
# Create Plot
plot = create_plot()
# Load Asset Glyphs
with open('asset_data.json', 'r') as f:
asset_json = json.loads(f.read())
for asset in asset_json['assets']:
plot_asset(plot, asset)
# Display Plot
output_file("county_map.html")
show(plot)
def func(self, args):
applications = self.build_applications(args)
for (route, app) in applications.items():
doc = app.create_document()
if route == "/":
filename = "index.html"
else:
filename = route[1:] + ".html"
output_file(filename)
if args.show:
show(doc, new='tab')
else:
save(doc)
def start(self):
c = self.last_report()
b = [i for sub in c for i in sub]
graph = vform(*b)
s = '../Report' + '/' + 'report_%s.html' % self.build[0].replace('.', '_')
output_file(s, title=self.build[0] + '-' + self.devicename[0] + 'Report')
return show(graph)
def BernGrid(Theta,pTheta,Data):
'''
Theta is vector of values between 0 and 1.
pTheta is prior probability mass at each value of Theta
Data is vector of 0's and 1's.
'''
if np.any((Theta < 0)|(Theta > 1 )):
raise ValueError("Theta values must be between 0 and 1")
if np.any(pTheta < 0):
raise ValueError("pTheta values must be non-negative")
if not(math.isclose(math.fsum(pTheta),1)):
raise ValueError("pTheta values must sum to 1.0")
if not(np.all((Data == 0) | (Data == 1))):
raise ValueError("Data values must be 0 or 1")
z = np.sum(Data) # No of heads
N = len(Data)
# Compute the Bernoulli likelihood at each value of Theta:
Likelihood = np.multiply(Theta**z,(1-Theta)**(N-z))
## calculate the Posterior
p_Data= np.dot(np.multiply(Theta**z,(1-Theta)**(N-z)),pTheta)
Posterior = (Likelihood * pTheta)/p_Data
## plot the Prior
plot_prior = figure(plot_width=800, plot_height=250, title='Prior')
plot_prior.x_range = Range1d(0,1)
plot_prior.y_range = Range1d(0, max(np.append(pTheta,Posterior)))
plot_prior.xaxis.axis_label = 'Θ'
plot_prior.yaxis.axis_label = 'p(Θ)'
plot_prior.vbar(x=Theta, width=0.001, bottom=0,top=pTheta)
## Plot the likelihood
plot_likelihood = figure(plot_width=800, plot_height=250, title='Likelihood')
plot_likelihood.x_range = Range1d(0, 1)
plot_likelihood.y_range = Range1d(0, 1.1*max(Likelihood))
plot_likelihood.xaxis.axis_label = 'Θ'
plot_likelihood.yaxis.axis_label = 'p(D|Θ)'
plot_likelihood.vbar(x=Theta, width=0.001, bottom=0,top=Likelihood)
## Plot the Posterior
plot_posterior = figure(plot_width=800, plot_height=250, title='Posterior')
plot_posterior.x_range = Range1d(0,1)
plot_posterior.y_range = Range1d(0, max(np.append(pTheta,Posterior)))
plot_posterior.xaxis.axis_label = 'Θ'
plot_posterior.yaxis.axis_label = 'p(Θ|D)'
plot_posterior.vbar(x=Theta, width=0.001, bottom=0,top=Posterior)
show(column(plot_prior,plot_likelihood,plot_posterior))
def bar_chart(d, x, show=True, **kwargs):
"""Displays a bar chart for the occurrence of the given x-value.
This plot type is especially useful for plotting the occurrence of categorical data,
where only a small number (<= 10) of different values are present.
This function is directly calling the advanced bokeh bar chart type,
therefore no additional class is used.
Useful kwargs include: title, plot_height, plot_width."""
title = kwargs.pop("title", "Occurrence of {}".format(x))
p = Bar(d, x, values=x, agg="count", legend=False, title=title, **kwargs)
p.yaxis.axis_label = "Occurrence"
p.axis.axis_label_text_font_size = "14pt"
p.axis.major_label_text_font_size = "14pt"
p.title.text_font_size = "18pt"
if show:
io.show(p)
else:
return p
def get_trains_week(stat_code):
sbn.set_style("white")
stat_vals = dis_trains[dis_trains.code == stat_code]
all_trains = stat_vals.times.values
xx = all_trains
days = np.array(xx[0])/1440
tot_mins = np.array(xx[0])%1440
hour = tot_mins/60
mins = tot_mins % 60
train_time = zip(days,hour,mins)
hist, edges = np.histogram(xx[0], bins = range(0,10081,120))
d = np.sin(3*gradient)
fig.image(image = [d],x = 0, y = 0, dw = 10080, dh = max(hist)+1)
fig.quad(top=hist, bottom=0, left=edges[:-1],right=edges[1:],fill_color="#036564",line_color="#033649")
fig.xaxis[0].ticker=FixedTicker(ticks=[])
fig.xaxis.major_label_orientation = "vertical"
# output_file("test_bg_image.html", title = "Background image")
show(fig)
def test_inline_extension():
from bokeh.io import show
from bokeh.models import TickFormatter
from bokeh.plotting import figure
from bokeh.util.compiler import TypeScript
TS_CODE = """
import {TickFormatter} from "models/formatters/tick_formatter"
export class TestFormatter extends TickFormatter {
doFormat(ticks: number[]): string[] {
if (ticks.length == 0)
return[]
else {
const formatted = [`${ticks[0]}`]
for (let i = 1; i < ticks.length; i++) {
const difference = (ticks[i] - ticks[0]).toPrecision(2)
formatted.push(`+${difference}}`)
}
return formatted
}
}
static initClass(): void {
this.prototype.type = "TestFormatter"
}
}
TestFormatter.initClass()
"""
class TestFormatter(TickFormatter):
__implementation__ = TypeScript(TS_CODE)
class TestFormatter2(TickFormatter):
__implementation__ = TypeScript("^") # invalid syntax on purpose
p = figure()
p.circle([1, 2, 3, 4, 6], [5, 7, 3, 2, 4])
p.xaxis.formatter = TestFormatter()
show(p)
def show_skyview_widget(tpf,
notebook_url='localhost:8888',
magnitude_limit=18):
"""skyview
Parameters
----------
tpf : lightkurve.TargetPixelFile
Target Pixel File to interact with
notebook_url: str
Location of the Jupyter notebook page (default: "localhost:8888")
When showing Bokeh applications, the Bokeh server must be
explicitly configured to allow connections originating from
different URLs. This parameter defaults to the standard notebook
host and port. If you are running on a different location, you
will need to supply this value for the application to display
properly. If no protocol is supplied in the URL, e.g. if it is
of the form "localhost:8888", then "http" will be used.
magnitude_limit : float
A value to limit the results in based on Gaia Gmag. Default, 18.
"""
try:
import bokeh
if bokeh.__version__[0] == '0':
warnings.warn("interact_sky() requires Bokeh version 1.0 or later",
LightkurveWarning)
except ImportError:
log.error(
"The interact_sky() tool requires the `bokeh` Python package; "
"you can install bokeh using e.g. `conda install bokeh`.")
return None
# Try to identify the "fiducial frame", for which the TPF WCS is exact
zp = (tpf.pos_corr1 == 0) & (tpf.pos_corr2 == 0)
zp_loc, = np.where(zp)
if len(zp_loc) == 1:
fiducial_frame = zp_loc[0]
else:
fiducial_frame = 0
def create_interact_ui(doc):
# The data source includes metadata for hover-over tooltips
tpf_source = None
# Create the TPF figure and its stretch slider
pedestal = np.nanmin(tpf.flux)
fig_tpf, stretch_slider = make_tpf_figure_elements(
tpf,
tpf_source,
pedestal=pedestal,
fiducial_frame=fiducial_frame,
plot_width=640,
plot_height=600)
fig_tpf, r = add_gaia_figure_elements(tpf,
fig_tpf,
magnitude_limit=magnitude_limit)
# Optionally override the default title
if tpf.mission == 'K2':
fig_tpf.title.text = "Skyview for EPIC {}, K2 Campaign {}, CCD {}.{}".format(
tpf.targetid, tpf.campaign, tpf.module, tpf.output)
elif tpf.mission == 'Kepler':
fig_tpf.title.text = "Skyview for KIC {}, Kepler Quarter {}, CCD {}.{}".format(
tpf.targetid, tpf.quarter, tpf.module, tpf.output)
elif tpf.mission == 'TESS':
fig_tpf.title.text = 'Skyview for TESS {} Sector {}, Camera {}.{}'.format(
tpf.targetid, tpf.sector, tpf.camera, tpf.ccd)
# Layout all of the plots
widgets_and_figures = layout([fig_tpf, stretch_slider])
doc.add_root(widgets_and_figures)
output_notebook(verbose=False, hide_banner=True)
return show(create_interact_ui, notebook_url=notebook_url)
def plot_close(d):
## Hovertool does so that when your mouse 'hovers' over the graph price and date is shown
hover = HoverTool(tooltips=[('Price','@Adj_Close{0,0.0}'),('Volume','@Volume{0,0.}'),('Date','@Date{%F}')] ,formatters = {'Date':'datetime'})
# $y{0,0.0} is formatiing, "0," defines value y with comma (like 1000 is 1,000) and "0.0" is one decimal
# @x{%F} defines value x and use format option, fomatters then define that we use datetime format,
# since the x-value is the date.
## tools allows you to pan around, zoom in (you have to choose the boxzoom option in the graph then
# 'mark' area you wish to view)
## reset to original position (there is no zoom in, besides this option),
# and save a the graph as a picture
tools="pan,box_zoom,reset,save"
# Make a list of companys we have data for
stock_list = list(d.columns.levels[0])
# Choose our inital stock
stock = list(d.columns.levels[0])[0]
# This line creates a source for bokeh plotting with our chosen stock
stocksource = ColumnDataSource(d[stock])
# We initialize our figure with titles, labels and specify that we want to use our tools mentioned above
p = figure(x_axis_type='datetime',title=f'Closing price of {stock}', \
tools=[hover,tools], y_axis_label='Closing price', x_axis_label='Date')
# Plot a line with the adjusted close plices, we reference our stocksource, that contains data for our choosen stock
p.line(x='Date', y='Adj_Close', source=stocksource, color = 'blue', legend= 'Closing price')
# We locate the legend in the top left, stocks mostly go from bottom left corner to top right corner
# so we figured this was a good location
p.legend.location = "top_left"
# visuals
p.ygrid.minor_grid_line_color = 'navy'
p.ygrid.minor_grid_line_alpha = 0.1
# formatting y-axis:
p.yaxis.formatter=NumeralTickFormatter(format='0,0')
# Defines a function that updates the plot when a different stock is chosen
def update_name(stock):
p.title.text = f'Closing price of {stock}'
# Updates the data
stocksource.data = ColumnDataSource(d[str(stock)]).data
# I can't for the life of my explain why .data needs to there on both side of the equal sign
# both they do
# push_notebook is af bokeh->jupyter-specific comand to tell python to update the bokeh plot in jupyter
push_notebook()
# show the plot, notebook_handle is again bokeh->jupyter-specific to show the plot in the notebook
show(p,notebook_handle=True)
# Make a dropdown-widget, so the user can choose different stocks, the layout option, makes the options box wider
# the style options make the desciption box wide enough for the description string to be read fully
drop_down = widgets.Dropdown(options=stock_list, layout = {'width':'50%'},\
description='Choose a stock or index:',style = {'description_width': 'initial'})
# Call the function
interact(update_name, stock = drop_down)
pv_share = len(pv) / len(firms_match)
shares = [both_share, parser_share, pv_share]
x = [1, 2, 3]
ticks = {1: "both", 2: "Parser", 3: "Patentsview"}
#* PLOT
plot = figure(plot_width=500,
plot_height=500,
title="Share of firm matches; total number of firms: 742518",
x_axis_label="Datasource",
y_axis_label="Percentage")
plot.vbar(x=x, top=shares, width=0.9)
plot.xaxis.ticker = list(ticks.keys())
plot.xaxis.major_label_overrides = ticks
plot.xaxis.major_label_orientation = 0.8
show(plot)
export_png(plot, filename="output/tmp/match_pv.png")
#* HOW MANY OF MISSINGS IN PARSER ARE MATCHED NOW
pv_pats = pv[["patent_id", "organization"]]
pv_pats = pv_pats.drop_duplicates(subset=["patent_id"], keep="first")
dst_missings = pat_3[["pat"]]
match_missings = dst_missings.merge(pv_pats,
left_on="pat",
right_on="patent_id",
how="outer",
indicator=True)
"""
Only 474 patents added, strongly suggesting that the missing citations
are indeed data from other patent systems or non-patent citations.
"""
def _display_timeline_dict(data: dict,
**kwargs) -> figure: # noqa: C901, MC0001
"""
Display a timeline of events.
Parameters
----------
data : dict
Data points to plot on the timeline.
Need to contain:
Key - Name of data type to be displayed in legend
Value - dict of data containing:
data : pd.DataFrame
Data to plot
time_column : str
Name of the timestamp column
source_columns : list
List of source columns to use in tooltips
color: str
Color of datapoints for this data
Other Parameters
----------------
ref_time : datetime, optional
Input reference line to display (the default is None)
title : str, optional
Title to display (the default is None)
time_column : str, optional
Name of the timestamp column
(the default is 'TimeGenerated')
legend: str, optional
Where to position the legend
None, left, right or inline (default is None)
yaxis : bool, optional
Whether to show the yaxis and labels
range_tool : bool, optional
Show the the range slider tool (default is True)
source_columns : list, optional
List of default source columns to use in tooltips
(the default is None)
height : int, optional
The height of the plot figure
(the default is auto-calculated height)
width : int, optional
The width of the plot figure (the default is 900)
Returns
-------
figure
The bokeh plot figure.
"""
reset_output()
output_notebook()
height: int = kwargs.pop("height", None)
width: int = kwargs.pop("width", 900)
ref_time: Any = kwargs.pop("ref_time", None)
ref_label: str = kwargs.pop("ref_label", None)
title: str = kwargs.pop("title", None)
legend_pos: str = kwargs.pop("legend", None)
show_yaxis: bool = kwargs.pop("yaxis", False)
show_range: bool = kwargs.pop("range_tool", True)
xgrid: bool = kwargs.pop("xgrid", True)
ygrid: bool = kwargs.pop("ygrid", False)
tool_tip_columns, min_time, max_time = _unpack_data_series_dict(
data, **kwargs)
series_count = len(data)
hover = HoverTool(
tooltips=_create_tool_tips(data, tool_tip_columns),
formatters={"Tooltip": "printf"},
)
title = f"Timeline: {title}" if title else "Event Timeline"
start_range = min_time - ((max_time - min_time) * 0.1)
end_range = max_time + ((max_time - min_time) * 0.1)
height = height if height else _calc_auto_plot_height(len(data))
y_range = ((-1 / series_count), series_count - 1 + (1 / series_count))
plot = figure(
x_range=(start_range, end_range),
y_range=y_range,
min_border_left=50,
plot_height=height,
plot_width=width,
x_axis_label="Event Time",
x_axis_type="datetime",
x_minor_ticks=10,
tools=[hover, "xwheel_zoom", "box_zoom", "reset", "save", "xpan"],
title=title,
)
plot.yaxis.visible = show_yaxis
if show_yaxis:
if data:
y_labels = {
ser_def["y_index"]: str(lbl)
for lbl, ser_def in data.items()
}
plot.yaxis.major_label_overrides = y_labels
if ygrid:
plot.ygrid.minor_grid_line_color = "navy"
plot.ygrid.minor_grid_line_alpha = 0.1
plot.ygrid.grid_line_color = "navy"
plot.ygrid.grid_line_alpha = 0.3
else:
plot.ygrid.grid_line_color = None
if xgrid:
plot.xgrid.minor_grid_line_color = "navy"
plot.xgrid.minor_grid_line_alpha = 0.3
else:
plot.xgrid.grid_line_color = None
# Create plot bar to act as as range selector
rng_select = _create_range_tool(
data=data,
min_time=min_time,
max_time=max_time,
plot_range=plot.x_range,
width=width,
height=height,
)
# set the tick datetime formatter
plot.xaxis[0].formatter = _get_tick_formatter()
if series_count > 1 and not legend_pos:
legend_pos = "left"
# plot groups individually so that we can create an interactive legend
# if legend_pos is "inline", we add add the normal legend inside the plot
# if legend_pos is "left" or "right", we add the legend to the side
legend_items = []
for ser_name, series_def in data.items():
if legend_pos == "inline":
p_series = plot.diamond(
x=series_def["time_column"],
y="y_index",
color=series_def["color"],
alpha=0.5,
size=10,
source=series_def["source"],
legend_label=str(ser_name),
)
else:
p_series = plot.diamond(
x=series_def["time_column"],
y="y_index",
color=series_def["color"],
alpha=0.5,
size=10,
source=series_def["source"],
)
if legend_pos in ["left", "right"]:
legend_items.append((str(ser_name), [p_series]))
if legend_pos == "inline":
# Position the inline legend
plot.legend.location = "center_left"
plot.legend.click_policy = "hide"
elif legend_pos in ["left", "right"]:
# Create the legend box outside of the plot area
ext_legend = Legend(
items=legend_items,
location="center",
click_policy="hide",
label_text_font_size="8pt",
)
plot.add_layout(ext_legend, legend_pos)
if ref_time is not None:
_add_ref_line(plot, ref_time, ref_label, len(data))
if show_range:
show(column(plot, rng_select))
else:
show(plot)
return plot
style="float: left; margin: 0px 15px 15px 0px;"
border="2"
></img>
</div>
<div>
<span style="font-size: 15px; font-weight: bold;">@species</span>
</div>
<div>
<span style="font-size: 10px; color: #696;">Petal length: @petal_length</span><br>
<span style="font-size: 10px; color: #696;">Petal width: @petal_width</span>
</div>
</div>
""")
f.add_tools(hover)
f.toolbar_location="above"
f.toolbar.logo=None
#Style the legend
f.legend.location = (575,555)
f.legend.location = 'top_left'
f.legend.background_fill_alpha = 0
f.legend.border_line_color = None
f.legend.margin = 10
f.legend.padding = 18
f.legend.label_text_color = 'olive'
f.legend.label_text_font = 'times'
#Save and show the figure
show(f)
tooltips=[('date', '@Month @Year'), ('rate', '@rate%')])
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_text_font_size = "5pt"
p.axis.major_label_standoff = 0
p.xaxis.major_label_orientation = pi / 3
p.rect(x="Year",
y="Month",
width=1,
height=1,
source=df,
fill_color={
'field': 'rate',
'transform': mapper
},
line_color=None)
color_bar = ColorBar(color_mapper=mapper,
major_label_text_font_size="5pt",
ticker=BasicTicker(desired_num_ticks=len(colors)),
formatter=PrintfTickFormatter(format="%d%%"),
label_standoff=6,
border_line_color=None,
location=(0, 0))
p.add_layout(color_bar, 'right')
show(p) # show the plot
def show_radar(dataframe):
"""Visualize lipid-protein contacts using a Bokeh radar map.
This is useful if you want to (i) compare the binding profile of two residues and
(ii) when you want to see how different contact metrics compare against each other.
Parameters
----------
dataframe : pd.DataFrame
A contacts dataframe. This will be the output of pl.contacts_dataframe() command.
"""
output_notebook()
def radarApp(doc):
df = dataframe
gpcrs = list(df.Protein.unique())
lipids = list(df.Lipids.unique())
radius = list(df.Radius.unique())
radius = [str(r) for r in radius]
# Normalize [0-1] all contact parameters with respect to each other.
for cmn in list(df.columns)[:-5]:
for lipid in lipids:
for radius_value in radius:
radius_value = float(radius_value)
dfmin = df[(df.Lipids == lipid)
& (df.Radius == radius_value)][cmn].min()
dfmax = df[(df.Lipids == lipid)
& (df.Radius == radius_value)][cmn].max()
lip_index = list(df[(df.Lipids == lipid)
& (df.Radius == radius_value)].index)
df.loc[lip_index, cmn] = df[(df.Lipids == lipid) & (
df.Radius == radius_value)][cmn].apply(
lambda x: (x - dfmin) / (dfmax - dfmin))
df = df.fillna(0)
# 1 unique set of residues - works also if there's only 1 set available.
resname = df[(df.Protein == gpcrs[0]) & (df.Lipids == lipids[0]) &
(df.Radius == float(radius[0]))].ResName.to_list()
resid = df[(df.Protein == gpcrs[0]) & (df.Lipids == lipids[0]) &
(df.Radius == float(radius[0]))].ResID.to_list()
residues = []
for rn, ri in zip(resname, resid):
residues.append("{}-{}".format(rn, ri))
import random
# Create Input controls
gpcr1 = Select(title="Protein",
value=gpcrs[0],
options=gpcrs,
width=100)
gpcr2 = Select(title="Protein",
value=gpcrs[0],
options=gpcrs,
width=100)
lipid1 = Select(title="Lipid",
value=lipids[0],
options=lipids,
width=100)
lipid2 = Select(title="Lipid",
value=lipids[0],
options=lipids,
width=100)
residue1 = Select(title="Residue",
value=random.choice(residues),
options=residues,
width=120)
residue2 = Select(title="Residue",
value=random.choice(residues),
options=residues,
width=120)
radius1 = Select(title="Radius",
value=radius[0],
options=radius,
width=100)
radius2 = Select(title="Radius",
value=radius[0],
options=radius,
width=100)
# num_vars = 6
num_vars = len(list(df.columns)[:-5])
centre = 0.5
theta = np.linspace(0, 2 * np.pi, num_vars, endpoint=False)
theta += np.pi / 2
verts = unit_poly_verts(theta, centre)
xv = [v[0] for v in verts]
yv = [v[1] for v in verts]
f1 = df[(df.Protein == str(gpcr1.value))
& (df.Lipids == str(lipid1.value)) &
(df.ResID == int(str(residue1.value).split("-")[1])) &
(df.Radius == float(radius1.value)
)].loc[:, list(df.columns)[:num_vars]].to_numpy().reshape(
num_vars, )
f2 = df[(df.Protein == str(gpcr2.value))
& (df.Lipids == str(lipid2.value)) &
(df.ResID == int(str(residue2.value).split("-")[1])) &
(df.Radius == float(radius2.value)
)].loc[:, list(df.columns)[:num_vars]].to_numpy().reshape(
num_vars, )
flist = [f1, f2]
p = figure(plot_height=400,
plot_width=800,
x_range=(-0.3, 1.3),
y_range=(-0.3, 1.3),
tools="")
cmap = RdBu[num_vars]
colors = cmap[:1] + cmap[-1:]
patch1 = ColumnDataSource(data=dict(xi=[], yi=[]))
circle1 = ColumnDataSource(data=dict(xt=[], yt=[]))
xt, yt = radar_patch(f1, theta, centre)
xi, yi = star_curv(xt + xt[:1], yt + yt[:1])
patch = p.patch(x="xi",
y="yi",
fill_alpha=0.15,
fill_color=colors[0],
line_color=colors[0],
source=patch1)
circle = p.circle(x='xt',
y='yt',
size=10,
alpha=0.5,
line_color=colors[0],
fill_color=colors[0],
source=circle1)
patch2 = ColumnDataSource(data=dict(xi=[], yi=[]))
circle2 = ColumnDataSource(data=dict(xt=[], yt=[]))
xt, yt = radar_patch(f2, theta, centre)
xi, yi = star_curv(xt + xt[:1], yt + yt[:1])
patch = p.patch(x="xi",
y="yi",
fill_alpha=0.15,
fill_color=colors[1],
line_color=colors[1],
source=patch2)
circle = p.circle(x='xt',
y='yt',
size=10,
alpha=0.5,
line_color=colors[1],
fill_color=colors[1],
source=circle2)
# Draw grid so the plot looks like a polar graph.
text_label = list(df.columns)[:num_vars] + ['']
p.circle(x=0.5,
y=0.5,
size=20,
fill_alpha=0,
line_color='black',
line_dash='dashed',
line_alpha=0.2)
for size in [x * 100 for x in range(1, 10)]:
p.circle(x=0.5,
y=0.5,
size=size,
fill_alpha=0,
line_color='black',
line_dash='dashed',
line_alpha=0.2)
line = np.linspace(-2, 2, 100)
p.line(line, (line * 0.58) + 0.21,
line_color='black',
line_dash='dashed',
line_alpha=0.2)
p.line(line, (line * (-0.58)) + 0.79,
line_color='black',
line_dash='dashed',
line_alpha=0.2)
p.line([0.5] * 100,
line,
line_color='black',
line_dash='dashed',
line_alpha=0.2)
# Hide axes.
p.xgrid.grid_line_color = None
p.ygrid.grid_line_color = None
p.xaxis.major_tick_line_color = None
p.xaxis.minor_tick_line_color = None
p.yaxis.major_tick_line_color = None
p.yaxis.minor_tick_line_color = None
p.xaxis.major_label_text_font_size = '0pt'
p.yaxis.major_label_text_font_size = '0pt'
p.axis.visible = None
p.toolbar.logo = None
p.toolbar_location = None
# Draw the hexagon with labels attached.
p.line(x=xv + [centre], y=yv + [1], color='black')
xv[1] = xv[1] - 0.13
xv[2] = xv[2] - 0.1
xv[-2] = xv[-2] + 0.16
xv[-1] = xv[-1] + 0.1
# yv[3] = yv[3] - 0.06
label_source = ColumnDataSource({
'x': xv + [centre],
'y': yv + [1],
'text': text_label
})
labels = LabelSet(x="x",
y="y",
text="text",
source=label_source,
level='glyph',
text_align="center")
p.add_layout(labels)
def select_dfGPCR():
gpcr1_val, gpcr2_val = gpcr1.value, gpcr2.value
lipid1_val, lipid2_val = lipid1.value, lipid2.value
res1_val, res2_val = str(residue1.value).split("-")[1], str(
residue2.value).split("-")[1]
f1 = df[(df.Protein == str(gpcr1_val))
& (df.Lipids == str(lipid1_val)) &
(df.ResID == int(res1_val)) &
(df.Radius == float(radius1.value)
)].loc[:, list(df.columns)[:num_vars]].to_numpy().reshape(
num_vars, )
f2 = df[(df.Protein == str(gpcr2_val))
& (df.Lipids == str(lipid2_val)) &
(df.ResID == int(res2_val)) &
(df.Radius == float(radius2.value)
)].loc[:, list(df.columns)[:num_vars]].to_numpy().reshape(
num_vars, )
return (f1, f2)
def update1():
gpcr_val = gpcr1.value
lipid1_val = lipid1.value
radius1_val = radius1.value
resname = df[(df.Protein == str(gpcr_val))
& (df.Lipids == str(lipid1_val)) &
(df.Radius == float(radius1_val))].ResName.to_list()
resid = df[(df.Protein == str(gpcr_val))
& (df.Lipids == str(lipid1_val)) &
(df.Radius == float(radius1_val))].ResID.to_list()
residues = []
for rn, ri in zip(resname, resid):
residues.append("{}-{}".format(rn, ri))
residue1.options = residues
if residue1.value not in residues:
residue1.value = residues[0]
f1 = select_dfGPCR()[0]
xt, yt = radar_patch(f1, theta, centre)
xi, yi = star_curv(xt + xt[:1], yt + yt[:1])
circle1.data = dict(xt=xt, yt=yt)
patch1.data = dict(xi=xi, yi=yi)
def update2():
gpcr_val = gpcr1.value
lipid2_val = lipid2.value
radius2_val = radius2.value
resname = df[(df.Protein == str(gpcr_val))
& (df.Lipids == str(lipid2_val)) &
(df.Radius == float(radius2_val))].ResName.to_list()
resid = df[(df.Protein == str(gpcr_val))
& (df.Lipids == str(lipid2_val)) &
(df.Radius == float(radius2_val))].ResID.to_list()
residues = []
for rn, ri in zip(resname, resid):
residues.append("{}-{}".format(rn, ri))
# options = [str(x) for x in options]
residue2.options = residues
if residue2.value not in residues:
residue2.value = residues[0]
f2 = select_dfGPCR()[1]
xt, yt = radar_patch(f2, theta, centre)
xi, yi = star_curv(xt + xt[:1], yt + yt[:1])
circle2.data = dict(xt=xt, yt=yt)
patch2.data = dict(xi=xi, yi=yi)
controls1 = [gpcr1, lipid1, residue1, radius1]
controls2 = [gpcr2, lipid2, residue2, radius2]
for control1 in controls1:
control1.on_change('value', lambda attr, old, new: update1())
for control2 in controls2:
control2.on_change('value', lambda attr, old, new: update2())
inputs1 = column([gpcr1, lipid1, residue1, radius1])
inputs2 = column([gpcr2, lipid2, residue2, radius2])
l = layout([[inputs1, p, inputs2]])
update1()
update2()
doc.add_root(l)
doc.title = "Radar App"
doc.theme = Theme(json=yaml.load("""
attrs:
Figure:
toolbar_location: above
height: 500
width: 800
Grid:
grid_line_dash: [6, 4]
grid_line_color: black
""",
Loader=yaml.FullLoader))
return show(radarApp)
def CNV_Map(df,
sample_order=[],
title="CN heatmaps sorted by SMAD4 loss, pointing VPS4B",
width=900,
height=400,
standoff=10,
y_label='',
marks=[]):
"""
create an interactive plot suited for visualizing segment level CN data for a set of samples using bokeh
args:
----
df: df['Sample' 'Start' 'End' 'Segment_Mean' 'size'] the df containing segment level
copy number (can be subsetted to a specific region or genome-wide)
sampleorder: list[Sample] <- for all samples present in the df
title: plot title
width: int width
height: int height
standoff: the space between the plot and the x axis
y_label: the y axis label
marks: location of lines at specific loci
Returns:
--------
The bokeh object
"""
colors = [
"#75968f", "#a5bab7", "#c9d9d3", "#e2e2e2", "#dfccce", "#ddb7b1",
"#cc7878", "#933b41", "#550b1d"
]
colors = RdBu[8]
mapper = LinearColorMapper(palette=colors,
low=df.Segment_Mean.min(),
high=df.Segment_Mean.max())
if len(sample_order) == 0:
sample_order = list(set(df.Sample.tolist()))
TOOLS = "hover,save,pan,box_zoom,reset,wheel_zoom"
p = figure(title=title,
y_range=(df.End.max(), df.Start.min()),
x_range=sample_order,
x_axis_location="above",
plot_width=width,
plot_height=height,
tools=TOOLS,
toolbar_location='below',
tooltips=[('pos', '@Start, @End'), ('relative CN', '@Sample')])
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_text_font_size = "5pt"
p.axis.major_label_standoff = standoff
p.xaxis.major_label_orientation = pi / 3
pos = 0
# for i,val in enumerate(historder):
# p.rect(x=pos,y=-7,width=len(orderbyhist[val]), height=10, fill_color=small_palettes['Viridis'][4][i])
# p.text(x=pos+len(orderbyhist[val])/2, y=-9, text=str(val), text_color="#96deb3")
# pos += len(orderbyhist[val])
p.rect(x="Sample",
y="Start",
width=0.9,
height="size",
source=df.reset_index(drop=True),
fill_color={
'field': 'Segment_Mean',
'transform': mapper
},
line_color=None)
color_bar = ColorBar(color_mapper=mapper,
major_label_text_font_size="5pt",
ticker=BasicTicker(desired_num_ticks=len(colors)),
formatter=PrintfTickFormatter(format="%.2f"),
label_standoff=6,
border_line_color=None,
location=(0, 0))
p.add_layout(color_bar, 'right')
p.yaxis.axis_label = y_label
# p.yaxis.major_label_overrides={20:'Centromer'}
for val in marks:
hline = Span(location=val,
dimension='width',
line_color='green',
line_width=0.2)
p.renderers.extend([hline])
if folder:
save(p, folder + title.replace(' ', "_") + "_cn_plot.html")
#export_png(p, filename=folder + title.replace(' ', "_") + "_cn_plot.png")
show(p) # show the plot
return p
if __name__ == '__main__':
df = mercator_df()
fig = nyc_map('Citi bike stations in Jersey city and New york city')
# colors for Jersey city and NYC regions
fill_color = {70: 'blue', 71: 'firebrick'}
line_color = {70: 'blue', 71: 'firebrick'}
df["fill"] = df['region_id'].map(lambda x: fill_color[x])
df["line"] = df['region_id'].map(lambda x: line_color[x])
source = ColumnDataSource(df)
# circle glyph for the stations
region_glyph = Circle(x="x",
y="y",
fill_color="fill",
line_color="line",
size=10,
fill_alpha=0.5)
region = fig.add_glyph(source, region_glyph)
# hover tooltip to display name
tooltips = """
<div>
<span style="font-size: 15px;">@name</span> <br>
<span style="font-size: 15px;">station id: @station_id</span>
</div>
"""
# add hover tool to figure
hover = HoverTool(tooltips=tooltips, renderers=[region])
fig.add_tools(hover)
show(fig)
def scatter(data,
labels=None,
title='scatter plot',
showlabels=False,
folder='',
colors=None,
xname='',
yname="",
importance=None,
radi=5,
alpha=0.8,
**kwargs):
"""
Makes an interactive scatter plot using Bokeh
Args:
-----
data: array-like with shape [N,2]
labels: list[str] a list of N names for each points
title: str the plot title
showlabels: bool if the labels should be always displayed or not (else just on hover)
colors: list[int] of N integers from 0 up to 256 for the dot's colors
folder: str of location where to save the plot, won't save if empty
xname: str the name of the x axes
yname: str the name of the y axes
importance: a list[int] of N values to scale the size of the dots and their opacity by
radi: int the size of the dots
alpha: float the opacity of the dots
**kwargs: additional bokeh.figure args
Returns:
------
the bokeh object
"""
TOOLS = "hover,crosshair,pan,wheel_zoom,zoom_in,zoom_out,box_zoom,undo,redo,reset,save,box_select,lasso_select,"
col = viridis(len(set(colors))) if colors is not None else ['#29788E'
] # (viridis1)
radii = []
fill_alpha = []
cols = []
for i in range(data.shape[0]):
radii.append(radi if importance is None else radi / 2 +
importance[i] * 30)
fill_alpha.append(alpha if importance is None else alpha -
(0.2 * importance[i]))
cols.append(col[0] if colors is None else col[int(colors[i])])
source = ColumnDataSource(
data=dict(x=data[:, 0],
y=data[:, 1],
labels=labels if labels is not None else [''] * len(radii),
fill_color=cols,
fill_alpha=fill_alpha,
radius=radii))
TOOLTIPS = [
("name", "@labels"),
("(x,y)", "(@x, @y)"),
]
p = figure(tools=TOOLS, tooltips=TOOLTIPS, title=title)
p.circle('x',
'y',
color='fill_color',
fill_alpha='fill_alpha',
line_width=0,
radius='radius' if radi else None,
source=source)
p.xaxis[0].axis_label = xname
p.yaxis[0].axis_label = yname
if showlabels:
labels = LabelSet(x='x',
y='y',
text='labels',
level='glyph',
text_font_size='9pt',
x_offset=5,
y_offset=5,
source=source,
render_mode='canvas')
p.add_layout(labels)
try:
show(p)
except:
show(p)
if folder:
save(p, folder + title.replace(' ', "_") + "_scatter.html")
#export_png(p, filename=folder + title.replace(' ', "_") + "_scatter.png")
return p
def volcano(data,
folder='',
tohighlight=None,
tooltips=[('gene', '@gene_id')],
title="volcano plot",
xlabel='log-fold change',
ylabel='-log(Q)',
maxvalue=100,
searchbox=False,
logfoldtohighlight=0.15,
pvaltohighlight=0.1,
showlabels=False):
"""
Make an interactive volcano plot from Differential Expression analysis tools outputs
Args:
-----
data: a df with rows genes and cols [log2FoldChange, pvalue, gene_id]
folder: str of location where to save the plot, won't save if empty
tohighlight: list[str] of genes to highlight in the plot
tooltips: list[tuples(str,str)] if user wants tot specify another bokeh tooltip
title: str plot title
xlabel: str if user wants to specify the title of the x axis
ylabel: str if user wants tot specify the title of the y axis
maxvalue: float the max -log2(pvalue authorized usefull when managing inf vals)
searchbox: bool whether or not to add a searchBox to interactively highlight genes
logfoldtohighlight: float min logfoldchange when to diplay points
pvaltohighlight: float min pvalue when to diplay points
showlabels: bool whether or not to show a text above each datapoint with its label information
Returns:
--------
The bokeh object
"""
# pdb.set_trace()
to_plot_not, to_plot_yes = selector(
data, tohighlight if tohighlight is not None else [],
logfoldtohighlight, pvaltohighlight)
hover = HoverTool(tooltips=tooltips, names=['circles'])
# Create figure
p = figure(title=title, plot_width=650, plot_height=450)
p.xgrid.grid_line_color = 'white'
p.ygrid.grid_line_color = 'white'
p.xaxis.axis_label = xlabel
p.yaxis.axis_label = ylabel
# Add the hover tool
p.add_tools(hover)
p, source1 = add_points(p,
to_plot_not,
'log2FoldChange',
'pvalue',
color='#1a9641',
maxvalue=maxvalue)
p, source2 = add_points(p,
to_plot_yes,
'log2FoldChange',
'pvalue',
color='#fc8d59',
alpha=0.6,
outline=True,
maxvalue=maxvalue)
if showlabels:
labels = LabelSet(x='log2FoldChange',
y='transformed_q',
text_font_size='7pt',
text="gene_id",
level="glyph",
x_offset=5,
y_offset=5,
source=source2,
render_mode='canvas')
p.add_layout(labels)
if searchbox:
text = TextInput(title="text", value="gene")
text.js_on_change(
'value',
CustomJS(args=dict(source=source1),
code="""
var data = source.data
var value = cb_obj.value
var gene_id = data.gene_id
var a = -1
for (i=0; i < gene_id.length; i++) {
if ( gene_id[i]===value ) { a=i; console.log(i); data.size[i]=7; data.alpha[i]=1; data.color[i]='#fc8d59' }
}
source.data = data
console.log(source)
console.log(cb_obj)
source.change.emit()
console.log(source)
"""))
p = column(text, p)
if folder:
save(p, folder + title.replace(' ', "_") + "_volcano.html")
#export_png(p, filename=folder + title.replace(' ', "_") + "_volcano.png")
try:
show(p)
except:
show(p)
return p
def correlationMatrix(data,
names,
colors=None,
pvals=None,
maxokpval=10**-9,
other=None,
title="correlation Matrix",
dataIsCorr=False,
invert=False,
size=40,
folder='',
interactive=False,
maxval=None,
minval=None):
"""
Make an interactive correlation matrix from an array using bokeh
Args:
-----
data: arrayLike of int / float/ bool of size(names*val) or (names*names)
names: list[str] of names for each rows
colors: list[int] of size(names) a color for each names (good to display clusters)
pvals: arraylike of int / float/ bool of size(names*val) or (names*names) with the corresponding pvalues
maxokpval: float threshold when pvalue is considered good. otherwise lowers the size of the square
until 10**-3 when it disappears
other: arrayLike of int / float/ bool of size(names*val) or (names*names), an additional information
matrix that you want ot display with opacity whereas correlations willl be displayed with
title: str the plot title
dataIsCorr: bool if not true, we will compute the corrcoef of the data array
invert: bool whether or not to invert the matrix before running corrcoef
size: int the plot size
folder: str of folder location where to save the plot, won't save if empty
interactive: bool whether or not to make the plot interactive (else will use matplotlib)
maxval: float clamping coloring up to maxval
minval: float clamping coloring down to minval
Returns:
-------
the bokeh object if interactive else None
"""
if not dataIsCorr:
print("computing correlations")
data = np.corrcoef(np.array(data) if not invert else np.array(data).T)
else:
data = np.array(data)
regdata = data.copy()
if maxval is not None:
data[data > maxval] = maxval
data[data < -maxval] = -maxval
if minval is not None:
data[data < minval] = minval
data = data / data.max()
TOOLS = "hover,crosshair,pan,wheel_zoom,zoom_in,zoom_out,box_zoom,undo,redo,reset,save"
xname = []
yname = []
color = []
alpha = []
height = []
width = []
if type(colors) is list:
print('we are assuming you want to display clusters with colors')
elif other is not None:
print(
'we are assuming you want to display the other of your correlation with opacity'
)
if pvals is not None:
print(
'we are assuming you want to display the pvals of your correlation with size'
)
regpvals = pvals.copy()
u = pvals < maxokpval
pvals[~u] = np.log10(1 / pvals[~u])
pvals = pvals / pvals.max().max()
pvals[u] = 1
if interactive:
xname = []
yname = []
color = []
for i, name1 in enumerate(names):
for j, name2 in enumerate(names):
xname.append(name1)
yname.append(name2)
if pvals is not None:
height.append(max(0.1, min(0.9, pvals[i, j])))
color.append(cc.coolwarm[int(
max(0, (data[i, j] * 128) + 127))])
alpha.append(min(abs(data[i, j]), 0.9))
elif other is not None:
color.append(cc.coolwarm[int((data[i, j] * 128) + 127)])
alpha.append(
max(min(other[i,
j], 0.9), 0.1) if other[i,
j] != 0 else 0)
else:
alpha.append(min(abs(data[i, j]), 0.9))
if colors is not None:
if type(colors) is list:
if colors[i] == colors[j]:
color.append(Category10[10][colors[i]])
else:
color.append('lightgrey')
elif pvals is None and other is None:
color.append('grey' if data[i,
j] > 0 else Category20[3][2])
print(regdata.max())
if pvals is not None:
width = height.copy()
data = dict(xname=xname,
yname=yname,
colors=color,
alphas=alpha,
data=regdata.ravel(),
pvals=regpvals.ravel(),
width=width,
height=height)
else:
data = dict(xname=xname,
yname=yname,
colors=color,
alphas=alpha,
data=data.ravel())
tt = [('names', '@yname, @xname'), ('value', '@data')]
if pvals is not None:
tt.append(('pvals', '@pvals'))
p = figure(title=title if title is not None else "Correlation Matrix",
x_axis_location="above",
tools=TOOLS,
x_range=list(reversed(names)),
y_range=names,
tooltips=tt)
p.plot_width = 800
p.plot_height = 800
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_text_font_size = "5pt"
p.axis.major_label_standoff = 0
p.xaxis.major_label_orientation = np.pi / 3
p.rect('xname',
'yname',
width=0.9 if not width else 'width',
height=0.9 if not height else 'height',
source=data,
color='colors',
alpha='alphas',
line_color=None,
hover_line_color='black',
hover_color='colors')
save(p, folder + title.replace(' ', "_") + "_correlation.html")
#export_png(p, filename=folder + title.replace(' ', "_") + "_correlation.png")
try:
show(p)
except:
show(p)
return p # show the plot
else:
plt.figure(figsize=(size, 200))
plt.title('the correlation matrix')
plt.imshow(data)
plt.savefig(title + "_correlation.pdf")
plt.show()
def field_explorer(artifacts, points, fields_shp_path, html_file_out=''):
"""Create bokeh map with summary information about all fields
Parameters
----------
artifacts, points : pandas DataFrames
fields_shp_path : str
Path to the shapefile of fields
html_file_out : str
Path to save the output file
Returns
-------
None
Notes
-----
If you want to print the output in a Jupyter notebook, use
`from bokeh.io import output_notebook; output_notebook()`
before running the function.
"""
from bokeh.io import show
from bokeh.plotting import figure, output_file
from bokeh.models import (GeoJSONDataSource, HoverTool, PanTool,
WheelZoomTool, BoxZoomTool, ResetTool,
NumeralTickFormatter)
geo_artifacts = find_geo_field(
artifacts, fields_shp_path) # find geofield for artifacts
geo_points = find_geo_field(points,
fields_shp_path) # find geofield for points
fields_sum = fields_summary_table(
geo_points, geo_artifacts) # summarize artifacts by geofield
fields_shp = read_fields_shp(
fields_shp_path) # get fields shapefile as geodataframe
# attach artifact summaries to fields geodataframe
fields_merge = fields_shp.merge(fields_sum,
how='left',
left_on='fid',
right_on='Id')
fields_merge = fields_merge.rename(
columns={ # renaming columns makes them usable
'Polígono': 'polygon', # as tooltips in the bokeh plot
'Parcela': 'parcel',
'Subparcela': 'subparcel',
'Id': 'id',
'Núm. Pts.': 'n_pts',
'Núm. Frags.': 'n_frags',
'Pos. Pts.': 'pos_pts'
})
surveyed = fields_merge[
~fields_merge['n_pts'].isna()] # get separate dataframes for
unsurveyed = fields_merge[
fields_merge['n_pts'].isna()] # surveyed and unsurveyed fields
surveyed_geojson = surveyed.to_json() # convert both to geo_json
unsurveyed_geojson = unsurveyed.to_json()
surveyed_source = GeoJSONDataSource(
geojson=surveyed_geojson) # convert JSON to
unsurveyed_source = GeoJSONDataSource(
geojson=unsurveyed_geojson) # bokeh GeoJSONDataSource
output_file(html_file_out)
surveyed_hover = [('Status', 'surveyed'), ('Campo', '@fid'),
('Núm. Pts.', '@n_pts'), ('Pos. Pts.', '@pos_pts'),
('Núm. Frags.', '@n_frags')]
unsurveyed_hover = [('Status', 'not surveyed'), ('Campo', '@fid')]
p = figure(plot_width=600,
plot_height=450,
tools=[PanTool(),
WheelZoomTool(),
BoxZoomTool(),
ResetTool()])
p.xaxis[0].formatter = NumeralTickFormatter(format="0")
p.yaxis[0].formatter = NumeralTickFormatter(format="0")
s = p.patches(xs='xs',
ys='ys',
source=surveyed_source,
line_color='gray',
fill_color='lightgreen')
p.add_tools(HoverTool(renderers=[s], tooltips=surveyed_hover))
u = p.patches(xs='xs',
ys='ys',
source=unsurveyed_source,
line_color='gray',
fill_color='seashell')
p.add_tools(HoverTool(renderers=[u], tooltips=unsurveyed_hover))
show(p)
# CODE:
# Perform necessary imports
from bokeh.io import output_file, show
from bokeh.plotting import figure
from bokeh.models import HoverTool, ColumnDataSource
# Make the ColumnDataSource: source
source = ColumnDataSource(
data={
'x': data.loc[1970].fertility,
'y': data.loc[1970].life,
'country': data.loc[1970].Country,
})
# Create the figure: p
p = figure(title='1970',
x_axis_label='Fertility (children per woman)',
y_axis_label='Life Expectancy (years)',
plot_height=400,
plot_width=700,
tools=[HoverTool(tooltips='@country')])
# Add a circle glyph to the figure p
p.circle(x='x', y='y', source=source)
# Output the file and show the figure
output_file('gapminder.html')
show(p)
from bokeh.io import show from bokeh.layouts import gridplot from bokeh.layouts import layout # first line plot p1 = figure(plot_width=300, plot_height=150, title='first') p1.line([1, 2, 3, 4, 5], [6, 7, 8, 9, 10], color='blue') # second line plot p2 = figure(plot_width=300, plot_height=150, title='second') p2.line([6, 7, 8, 9, 10], [1, 2, 3, 4, 5], color='green') # third line plot p3 = figure(plot_width=300, plot_height=150, title='second') p3.line([6, 7, 3, 11, 10], [1, 2, 3, 2, 5], color='red') # pass 3 objects of plots to a grid layout grid = gridplot([[p1, p2], [p3]]) # # [0,0]: !null [0,1]: !null *[1,0]: null* [1,1]:!null # grid = gridplot([[p1, p2], [None, p3]]) # # span fits for a single column plot row # doc = layout([[p1, p2], [p3]], sizing_mode='scale_width') # pass the layout to show method instead plots show(grid)
from bokeh.io import output_file, show
from bokeh.layouts import column
from bokeh.plotting import figure
output_file("layout.html")
x = list(range(11))
y0 = x
y1 = [10 - i for i in x]
y2 = [abs(i - 5) for i in x]
# create three plots
s1 = figure(width=250, height=250, background_fill_color="#fafafa")
s1.circle(x, y0, size=12, color="#53777a", alpha=0.8)
s2 = figure(width=250, height=250, background_fill_color="#fafafa")
s2.triangle(x, y1, size=12, color="#c02942", alpha=0.8)
s3 = figure(width=250, height=250, background_fill_color="#fafafa")
s3.square(x, y2, size=12, color="#d95b43", alpha=0.8)
# put the results in a column and show
show(column(s1, s2, s3))
def draw(self):
graph = self.graph
N = len(graph.vertices)
node_indices = list(graph.vertices.keys())
plot = figure(title="Graph Layout Demonstration",
x_range=(-7, 7),
y_range=(-7, 7),
tools="",
toolbar_location=None)
graph_renderer = GraphRenderer()
graph_renderer.node_renderer.data_source.add(node_indices, 'index')
# node_colors = ['red'] * N
# graph.node_renderer.data_source.add(node_colors, 'color')
graph_renderer.node_renderer.glyph = Circle(radius=0.5,
fill_color="red")
edge_start = []
edge_end = []
# O(E), where E is the total number of edges
for vertex_id in node_indices:
for v in graph.vertices[vertex_id].edges:
edge_start.append(vertex_id)
edge_end.append(v)
graph_renderer.edge_renderer.data_source.data = dict(start=edge_start,
end=edge_end)
### start of layout code
# circ = [i*2*math.pi/8 for i in node_indices]
# x = [math.cos(i) for i in circ]
# y = [math.sin(i) for i in circ]
x = []
y = []
for vertex_id in node_indices:
vertex = graph.vertices[vertex_id]
x.append(vertex.x)
y.append(vertex.y)
graph_layout = dict(zip(node_indices, zip(x, y)))
graph_renderer.layout_provider = StaticLayoutProvider(
graph_layout=graph_layout)
plot.renderers.append(graph_renderer)
labelSource = ColumnDataSource(data=dict(
x=x, y=y, names=[vertex_id for vertex_id in graph.vertices]))
labels = LabelSet(x='x',
y='y',
text='names',
level='glyph',
text_align='center',
text_baseline='middle',
source=labelSource,
render_mode='canvas')
plot.add_layout(labels)
output_file('graph.html')
show(plot)
import networkx as nx
from bokeh.io import show, output_file
from bokeh.plotting import figure
from bokeh.models.graphs import from_networkx
G=nx.karate_club_graph()
plot = figure(title="Networkx Integration Demonstration", x_range=(-1.1,1.1), y_range=(-1.1,1.1),
tools="", toolbar_location=None)
graph = from_networkx(G, nx.spring_layout, scale=2, center=(0,0))
plot.renderers.append(graph)
output_file("networkx_graph.html")
show(plot)
def show(self):
self._plot.add_tools(*self._build_tools(self._df, *self._hover_args))
show(self._plot)
s.yaxis.axis_label_text_font_size = "14pt"
s.xaxis.axis_label_text_font_size = "14pt"
s.axis.major_label_text_font_size = "15pt"
odf = odf.sort_values("stars_per_employee", ascending=False)
t = figure(title="Number of Stars per Employee",
x_range=odf.corporate.unique(),
tools="",
toolbar_location=None,
plot_height=plot_height,
plot_width=plot_width)
t.vbar(source=odf,
x='corporate',
top='stars_per_employee',
width=1,
line_color='white',
fill_color=factor_cmap('corporate',
palette=colors,
factors=odf.corporate.unique()))
t.xaxis.major_label_orientation = pi / 3
t.x_range.range_padding = 0.01
t.y_range.range_padding = 0.01
# t.xgrid.grid_line_color = None
t.yaxis.axis_label_text_font_size = "14pt"
t.xaxis.axis_label_text_font_size = "14pt"
t.axis.major_label_text_font_size = "15pt"
show(column(row(p), row(s), row(t)))
from bokeh.layouts import gridplot
from bokeh.models.widgets import Tabs, Panel
from bokeh.layouts import column, row
#Read the Data File
TFGM = pd.read_csv('TSLA_F_GM.csv')
data = ColumnDataSource(TFGM)
TFGM['Date'] = pd.to_datetime(TFGM['Date'])
#plot1 Adjusted Closing Proces
plot1 = figure(x_axis_type = 'datetime', x_axis_label = 'Dates', y_axis_label = 'Adj. Close Price', title = '3 Stock Portfolio 10yr Adj. Close')
#plot1.line('datetime', 'Adj. Close Price', legend_label="some label")
plot1.line(x = TFGM['Date'], y = TFGM['GM_Adj Close'], color = 'red', legend_label='GM')
plot1.line(x = TFGM['Date'], y = TFGM['TSLA_Adj Close'], color = 'black', legend_label='TSLA')
plot1.line(x = TFGM['Date'], y = TFGM['F_Adj Close'], color = 'green', legend_label='F')
#plot1.line(x = TFGM['Date'], y = TFGM['S&P'], color = 'purple')
plot1.legend.location = "top_left"
output_file('PLOT001.html')
#plot2 high
plot2 = figure(x_axis_type = 'datetime', x_axis_label = 'Dates', y_axis_label = 'Volume', title = 'Volume')
plot2.line(x = TFGM['Date'], y = TFGM['GM_Volume'], color = 'red', legend_label='GM')
plot2.line(x = TFGM['Date'], y = TFGM['TSLA_Volume'], color = 'black', legend_label='TSLA')
plot2.line(x = TFGM['Date'], y = TFGM['F_Volume'], color = 'green', legend_label='F')
#plot2.line(x = TFGM['Date'], y = TFGM['S&P_RET'], color = 'purple')
plot2.legend.location = "top_left"
output_file('PLOT002.html')
#combined plots
row_layout = row(plot1, plot2)
output_file('twoplots.html')
show(row_layout)
def show_task_capacity_per_server(self):
from bokeh.io import output_file, show
from bokeh.models import GraphRenderer, Oval, StaticLayoutProvider, ColumnDataSource, LabelSet
from bokeh.plotting import figure
from bokeh.palettes import Category20c, Category20
# we have 12 kinds of tasks (number of columns in H) and 4 time_slots (number of rows in H)
number_of_servers = len(self.H)
tasks = ['task ' + str(i) for i in range(1, len(self.H[0]) + 1)]
index_array_of_tasks = list(range(1, len(tasks) + 1))
index_array_of_servers = list(range(len(tasks) + 1, len(tasks) + number_of_servers + 1))
number_of_tasks = len(tasks)
node_indices = np.concatenate((index_array_of_tasks, index_array_of_servers), axis=None).tolist()
node_x_location = np.concatenate((index_array_of_tasks, list(range(1, len(index_array_of_servers) + 1))),
axis=None).tolist()
node_y_location = np.concatenate(
(np.full(len(index_array_of_tasks), 5), np.full(len(index_array_of_servers), 3)), axis=None).tolist()
plot = figure(title='Task capacity per server', x_range=(0, max(number_of_servers, number_of_tasks) + 1),
y_range=(0, 8),
tools='', toolbar_location=None)
graph = GraphRenderer()
graph.node_renderer.data_source.add(node_indices, 'index')
graph.node_renderer.data_source.add(Category20c[len(node_indices)], 'color')
graph.node_renderer.glyph = Oval(height=0, width=0, fill_color='color')
network_graph_tasks_indices = []
network_graph_server_indices = []
network_graph_tasks_server_hash = {}
for k in range(number_of_servers): # servers
for j in range(number_of_tasks): # tasks
if self.H[k, j] > 0:
network_graph_tasks_indices.append(j + 1)
network_graph_server_indices.append(len(tasks) + k + 1)
network_graph_tasks_server_hash[j + 1] = self.H[k, j]
graph.edge_renderer.data_source.data = dict(
start=list(network_graph_tasks_indices),
end=list(network_graph_server_indices)
)
x = node_x_location
y = node_y_location
graph_layout = dict(zip(node_indices, zip(x, y)))
graph.layout_provider = StaticLayoutProvider(graph_layout=graph_layout)
plot.renderers.append(graph)
x_servers = list(range(1, len(index_array_of_servers) + 1))
y_servers = np.full(len(index_array_of_servers), 3)
plot.square(x_servers, y_servers, size=30, color=Category20[number_of_servers], alpha=0.5)
x_tasks = index_array_of_tasks
y_tasks = np.full(len(index_array_of_tasks), 5)
plot.circle(x_tasks, y_tasks, size=30, color=Category20[len(index_array_of_tasks)], alpha=0.5)
text_label_values = np.round(
np.multiply(np.round(list(network_graph_tasks_server_hash.values()), 2), 100)).tolist()
text_label_values = [str(int(capacity)) + '%' for capacity in text_label_values]
source = ColumnDataSource(data=dict(x=list(network_graph_tasks_server_hash.keys()),
y=np.full(len(network_graph_tasks_indices), 4.8),
values=text_label_values))
capacityLabels = LabelSet(x='x', y='y', text='values', level='glyph',
x_offset=-8, y_offset=10, source=source, render_mode='canvas', text_font_size="10pt")
plot.add_layout(capacityLabels)
source = ColumnDataSource(data=dict(x=[6, 6],
y=[2.5, 5.5],
values=['servers', 'tasks']))
typeLabel = LabelSet(x='x', y='y', text='values', level='glyph',
x_offset=0, y_offset=0, source=source, render_mode='canvas', text_font_size="10pt")
plot.add_layout(typeLabel)
output_file('graph.html')
show(plot)
return None
def show_flow_from_outside_to_buffers_to_tasks(self):
from bokeh.io import output_file, show
from bokeh.models import GraphRenderer, Oval, StaticLayoutProvider, ColumnDataSource, LabelSet, Arrow, OpenHead
from bokeh.plotting import figure
from bokeh.palettes import Plasma256
# vector alpha >0 , vector a can be any value
# a is input/output coming from outside
# alpha is initial value in buffer
# matrix G connected buffers and tasks
# in matrix G , flow between a task and multiple buffers
# a to buffer to task
number_of_io_nodes = len(self.a)
number_of_buffers = self.K
number_of_tasks = len(self.H[0])
index_array_of_io = list(range(1, number_of_io_nodes + 1))
index_array_of_buffers = list(range(number_of_io_nodes + 1, number_of_io_nodes + number_of_buffers + 1))
index_array_of_tasks = list(range(number_of_io_nodes + number_of_buffers + 1,
number_of_io_nodes + number_of_buffers + number_of_tasks + 1))
node_indices = np.concatenate((index_array_of_io, index_array_of_buffers, index_array_of_tasks),
axis=None).tolist()
node_x_location = np.concatenate((index_array_of_io, list(range(1, len(index_array_of_buffers) + 1)),
list(range(1, len(index_array_of_tasks) + 1))), axis=None).tolist()
node_y_location = np.concatenate(
(np.full(number_of_io_nodes, 7), np.full(number_of_buffers, 5), np.full(number_of_tasks, 3)),
axis=None).tolist()
max_x_range = max(number_of_io_nodes, number_of_buffers, number_of_tasks) + 1
plot = figure(title='Flow from outside to buffers to tasks', x_range=(0, max_x_range), y_range=(0, 9),
tools='', toolbar_location=None)
graph = GraphRenderer()
graph.node_renderer.data_source.add(node_indices, 'index')
graph.node_renderer.data_source.add(Plasma256[:len(node_indices)], 'color')
graph.node_renderer.glyph = Oval(height=0, width=0, fill_color='color')
start = index_array_of_io
end = index_array_of_buffers
network_graph_buffer_task_hash = {}
for buffer_index in range(number_of_buffers):
network_graph_buffer_task_hash[buffer_index + 1] = np.sum(self.G[buffer_index, :])
graph.edge_renderer.data_source.data = dict(
start=start,
end=end
)
x = node_x_location
y = node_y_location
graph_layout = dict(zip(node_indices, zip(x, y)))
graph.layout_provider = StaticLayoutProvider(graph_layout=graph_layout)
plot.renderers.append(graph)
x_io = list(range(1, number_of_io_nodes + 1))
y_io = np.full(number_of_io_nodes, 7)
plot.triangle(x_io, y_io, size=30, color=getLargePalette(number_of_io_nodes,Plasma256), alpha=0.5, line_width=2)
x_buffers = list(range(1, number_of_buffers + 1))
y_buffers = np.full(number_of_buffers, 5)
plot.rect(x_buffers, y_buffers, color=getLargePalette(number_of_buffers,Plasma256), alpha=0.5, width=0.5, height=0.5)
x_tasks = list(range(1, number_of_tasks + 1))
y_tasks = np.full(number_of_tasks, 3)
plot.circle(x_tasks, y_tasks, size=30, color=getLargePalette(number_of_tasks,Plasma256), alpha=0.5)
for i in range(number_of_buffers):
for j in range(number_of_tasks):
if self.G[i, j] > 0:
x_start_node = x_buffers[i]
y_start_node = y_buffers[i]
x_end_node = x_tasks[j]
y_end_node = y_tasks[j]
elif self.G[i, j] < 0:
x_start_node = x_tasks[j]
y_start_node = y_tasks[j]
x_end_node = x_buffers[i]
y_end_node = y_buffers[i]
plot.add_layout(Arrow(end=OpenHead(),
x_start=x_start_node, y_start=y_start_node, x_end=x_end_node, y_end=y_end_node))
text_label_values = np.round(
np.multiply(np.round(list(network_graph_buffer_task_hash.values()), 2), 100)).tolist()
text_label_values = [str(int(capacity)) + '%' for capacity in text_label_values]
source = ColumnDataSource(data=dict(x=list(network_graph_buffer_task_hash.keys()),
y=np.full(number_of_buffers, 4.8),
values=text_label_values))
capacityLabels = LabelSet(x='x', y='y', text='values', level='glyph',
x_offset=-8, y_offset=10, source=source, render_mode='canvas', text_font_size="10pt")
plot.add_layout(capacityLabels)
source = ColumnDataSource(data=dict(x=[max_x_range / 2 - 0.5, max_x_range / 2 - 0.5, max_x_range / 2 - 0.5],
y=[2.5, 5.5, 7.5],
values=['tasks', 'buffers', 'outside sources']))
typeLabel = LabelSet(x='x', y='y', text='values', level='glyph',
x_offset=0, y_offset=0, source=source, render_mode='canvas', text_font_size="10pt")
plot.add_layout(typeLabel)
output_file('graph.html')
show(plot)
return None
s2.data['z']=d2[cb_obj.selected['1d'].indices]
console.log(d2['z'])
s2.trigger('change');
console.log('Tap event occured at x-position: ' + cb_obj.selected['1d'].indices)
""")
#Creating a slider
slider = Slider(start=0,
end=14400,
value=0,
step=1,
title="Time slider in seconds")
def update(s1=s1, slider=slider, window=None):
data = s1.data
v = cb_obj.value
data['rate'] = data[v]
s1.trigger('change')
slider.js_on_change('value', CustomJS.from_py_func(update))
g1 = (column(
p,
widgetbox(slider),
))
g2 = column(sp, n)
layout = row(g1, g2)
show(layout)
# In[ ]:
def show_interact_widget(tpf,
notebook_url='localhost:8888',
max_cadences=30000,
aperture_mask='pipeline',
exported_filename=None):
"""Display an interactive Jupyter Notebook widget to inspect the pixel data.
The widget will show both the lightcurve and pixel data. The pixel data
supports pixel selection via Bokeh tap and box select tools in an
interactive javascript user interface.
Note: at this time, this feature only works inside an active Jupyter
Notebook, and tends to be too slow when more than ~30,000 cadences
are contained in the TPF (e.g. short cadence data).
Parameters
----------
tpf : lightkurve.TargetPixelFile
Target Pixel File to interact with
notebook_url: str
Location of the Jupyter notebook page (default: "localhost:8888")
When showing Bokeh applications, the Bokeh server must be
explicitly configured to allow connections originating from
different URLs. This parameter defaults to the standard notebook
host and port. If you are running on a different location, you
will need to supply this value for the application to display
properly. If no protocol is supplied in the URL, e.g. if it is
of the form "localhost:8888", then "http" will be used.
max_cadences : int
Raise a RuntimeError if the number of cadences shown is larger than
this value. This limit helps keep browsers from becoming unresponsive.
"""
try:
import bokeh
if bokeh.__version__[0] == '0':
warnings.warn("interact() requires Bokeh version 1.0 or later",
LightkurveWarning)
except ImportError:
log.error("The interact() tool requires the `bokeh` Python package; "
"you can install bokeh using e.g. `conda install bokeh`.")
return None
aperture_mask = tpf._parse_aperture_mask(aperture_mask)
if exported_filename is None:
exported_filename = make_default_export_name(tpf)
try:
exported_filename = str(exported_filename)
except:
log.error('Invalid input filename type for interact()')
raise
if ('.fits' not in exported_filename.lower()):
exported_filename += '.fits'
lc = tpf.to_lightcurve(aperture_mask=aperture_mask)
npix = tpf.flux[0, :, :].size
pixel_index_array = np.arange(0, npix, 1).reshape(tpf.flux[0].shape)
# Bokeh cannot handle many data points
# https://github.com/bokeh/bokeh/issues/7490
if len(lc.cadenceno) > max_cadences:
msg = 'Interact cannot display more than {} cadences.'
raise RuntimeError(msg.format(max_cadences))
def create_interact_ui(doc):
# The data source includes metadata for hover-over tooltips
lc_source = prepare_lightcurve_datasource(lc)
tpf_source = prepare_tpf_datasource(tpf, aperture_mask)
# Create the lightcurve figure and its vertical marker
fig_lc, vertical_line = make_lightcurve_figure_elements(lc, lc_source)
# Create the TPF figure and its stretch slider
pedestal = np.nanmin(tpf.flux)
fig_tpf, stretch_slider = make_tpf_figure_elements(tpf,
tpf_source,
pedestal=pedestal,
fiducial_frame=0)
# Helper lookup table which maps cadence number onto flux array index.
tpf_index_lookup = {cad: idx for idx, cad in enumerate(tpf.cadenceno)}
# Interactive slider widgets and buttons to select the cadence number
cadence_slider = Slider(start=np.min(tpf.cadenceno),
end=np.max(tpf.cadenceno),
value=np.min(tpf.cadenceno),
step=1,
title="Cadence Number",
width=490)
r_button = Button(label=">", button_type="default", width=30)
l_button = Button(label="<", button_type="default", width=30)
export_button = Button(label="Save Lightcurve",
button_type="success",
width=120)
message_on_save = Div(text=' ', width=600, height=15)
# Callbacks
def update_upon_pixel_selection(attr, old, new):
"""Callback to take action when pixels are selected."""
# Check if a selection was "re-clicked", then de-select
if ((sorted(old) == sorted(new)) & (new != [])):
# Trigger recursion
tpf_source.selected.indices = new[1:]
if new != []:
selected_indices = np.array(new)
selected_mask = np.isin(pixel_index_array, selected_indices)
lc_new = tpf.to_lightcurve(aperture_mask=selected_mask)
lc_source.data['flux'] = lc_new.flux
ylims = get_lightcurve_y_limits(lc_source)
fig_lc.y_range.start = ylims[0]
fig_lc.y_range.end = ylims[1]
else:
lc_source.data['flux'] = lc.flux * 0.0
fig_lc.y_range.start = -1
fig_lc.y_range.end = 1
message_on_save.text = " "
export_button.button_type = "success"
def update_upon_cadence_change(attr, old, new):
"""Callback to take action when cadence slider changes"""
if new in tpf.cadenceno:
frameno = tpf_index_lookup[new]
fig_tpf.select('tpfimg')[0].data_source.data['image'] = \
[tpf.flux[frameno, :, :] - pedestal]
vertical_line.update(location=tpf.time[frameno])
else:
fig_tpf.select('tpfimg')[0].data_source.data['image'] = \
[tpf.flux[0, :, :] * np.NaN]
lc_source.selected.indices = []
def go_right_by_one():
"""Step forward in time by a single cadence"""
existing_value = cadence_slider.value
if existing_value < np.max(tpf.cadenceno):
cadence_slider.value = existing_value + 1
def go_left_by_one():
"""Step back in time by a single cadence"""
existing_value = cadence_slider.value
if existing_value > np.min(tpf.cadenceno):
cadence_slider.value = existing_value - 1
def save_lightcurve():
"""Save the lightcurve as a fits file with mask as HDU extension"""
if tpf_source.selected.indices != []:
selected_indices = np.array(tpf_source.selected.indices)
selected_mask = np.isin(pixel_index_array, selected_indices)
lc_new = tpf.to_lightcurve(aperture_mask=selected_mask)
lc_new.to_fits(exported_filename,
overwrite=True,
aperture_mask=selected_mask.astype(np.int),
SOURCE='lightkurve interact',
NOTE='custom mask',
MASKNPIX=np.nansum(selected_mask))
if message_on_save.text == " ":
text = '<font color="black"><i>Saved file {} </i></font>'
message_on_save.text = text.format(exported_filename)
export_button.button_type = "success"
else:
text = '<font color="gray"><i>Saved file {} </i></font>'
message_on_save.text = text.format(exported_filename)
else:
text = '<font color="gray"><i>No pixels selected, no mask saved</i></font>'
export_button.button_type = "warning"
message_on_save.text = text
def jump_to_lightcurve_position(attr, old, new):
if new != []:
cadence_slider.value = lc.cadenceno[new[0]]
# Map changes to callbacks
r_button.on_click(go_right_by_one)
l_button.on_click(go_left_by_one)
tpf_source.selected.on_change('indices', update_upon_pixel_selection)
lc_source.selected.on_change('indices', jump_to_lightcurve_position)
export_button.on_click(save_lightcurve)
cadence_slider.on_change('value', update_upon_cadence_change)
# Layout all of the plots
sp1, sp2, sp3, sp4 = (Spacer(width=15), Spacer(width=30),
Spacer(width=80), Spacer(width=60))
widgets_and_figures = layout([fig_lc, fig_tpf], [
l_button, sp1, r_button, sp2, cadence_slider, sp3, stretch_slider
], [export_button, sp4, message_on_save])
doc.add_root(widgets_and_figures)
output_notebook(verbose=False, hide_banner=True)
return show(create_interact_ui, notebook_url=notebook_url)
def bigScatter(data,
precomputed=False,
logscale=False,
features=False,
title="BigScatter",
binsize=0.1,
folder="",
showpoint=False):
"""
uses a binning method to display millions of points at the same time and showcase density.
Does this in an interactive fashion
Args:
-----
data: array like. the array containing the point location x,y or their location and density of bins (q,r,c)
precomputed: bool whether or not the array has aleady been hexbined
logscale: bool, whether or not the data is logscaled
features: list[] if the matrix contains a feature column with feature information (names, values. for each bin/dot)
title: str the title of the plot
binsize: float the size of the bins
showpoint: bool whether or not to display them as points or hexes.
folder: str of location where to save the plot, won't save if empty
Returns:
------
the bokeh object
"""
TOOLS = "wheel_zoom,zoom_in,zoom_out,box_zoom,undo,redo,reset,save,box_select,lasso_select,"
names = [("count", "@c")]
if features:
names.append(('features', '@features'))
if precomputed:
TOOLS = "hover," + TOOLS
p = figure(title=title,
tools=TOOLS,
tooltips=names if precomputed else None,
match_aspect=True,
background_fill_color='#440154')
if precomputed:
p.hex_tile(q="q",
r="r",
size=binsize,
line_color=None,
source=data,
hover_color="pink",
hover_alpha=0.8,
fill_color=linear_cmap('c', 'Viridis256', 0, max(data.c))
if not logscale else {
'field': 'c',
'transform': LogColorMapper('Viridis256')
})
else:
if features:
print("we cannot yet process features on non precomputed version")
r, bins = p.hexbin(data[:, 0],
data[:, 1],
line_color=None,
size=binsize,
hover_color="pink",
hover_alpha=0.8,
fill_color=linear_cmap('c', 'Viridis256', 0, None)
if not logscale else {
'field': 'c',
'transform': LogColorMapper('Viridis256')
})
p.grid.visible = False
if showpoint:
p.circle(data[:, 0], data[:, 1], color="white", size=1)
if not precomputed:
p.add_tools(
HoverTool(tooltips=names,
mode="mouse",
point_policy="follow_mouse",
renderers=[r] if not precomputed else None))
try:
show(p)
except:
show(p)
if folder:
save(p, folder + title.replace(' ', "_") + "_scatter.html")
#export_png(p, filename=folder + title.replace(' ', "_") + "_scatter.png")
return p
from bokeh.io import show
from bokeh.models import Div
div = Div(
width=400, height=100, background="#fafafa",
text="The Pythagorean identity is $$\sin^2(x) + \cos^2(x) = 1$$"
)
show(div)
def create_cws_map(df, suffix):
"""Reads in a data-frame and exports a html file, containing a bokeh map, placed within the 'maps' folder.
Parameters
----------
df : dataframe
A dataframe that must contain the following columns:
- geometry
- p_id
- lon
- lat
- ta_int
suffix : str
A string that will be appended to the title of the plots as well as the html file-names.
"""
tile_provider = get_provider(
"CARTODBPOSITRON_RETINA"
) # More Providers https://docs.bokeh.org/en/latest/docs/reference/tile_providers.html
# Range bounds supplied in web mercator coordinates
p = figure(
x_range=(825000, 833000),
y_range=(5933000, 5935000),
x_axis_type="mercator",
y_axis_type="mercator", # Changes axis to a more legible input
x_axis_label="Longitude",
y_axis_label="Latitude",
sizing_mode="stretch_both")
p.add_tile(tile_provider)
# Filter point sto be added by color
p = filter_points_by_color(df, p)
# Add hover tools as a means for interactivity
my_hover = HoverTool(
) # https://automating-gis-processes.github.io/2016/Lesson5-interactive-map-bokeh.html#adding-interactivity-to-the-map
# Specify what parameters should be displayed when hovering
my_hover.tooltips = [('Id', '@p_id'), ('Temperature [C]', '@ta_int'),
('Longitude', '@lon'), ('Latitude', '@lat')]
p.add_tools(my_hover)
# Creating divs to serve as additional information
div_title = Div(align="center",
text="<h1>Citizen Weather Stations: " + suffix +
":00</h1>",
sizing_mode="stretch_both")
div_subtitle = Div(
align="center",
text=
"Blue: Below 22 °C. <br> Orange: Between 22 °C and 28 °C. <br> Red: Above 28 °C.",
sizing_mode="stretch_both")
# Arrange all the bokeh elements in a layout
layout_plot = layout([[div_title], [div_subtitle], [p]])
# Specify output location and name
output_file("../maps/Bern-CWS-Map_" + suffix + ".html")
# Shows the result in the default browser and saves the file
show(layout_plot)
def display_timeline_values(
data: pd.DataFrame,
y: str,
time_column: str = "TimeGenerated",
source_columns: list = None,
**kwargs,
) -> figure:
"""
Display a timeline of events.
Parameters
----------
data : pd.DataFrame
DataFrame as a single data set or grouped into individual
plot series using the `group_by` parameter
time_column : str, optional
Name of the timestamp column
(the default is 'TimeGenerated')
y : str
The column name holding the value to plot vertically
source_columns : list, optional
List of default source columns to use in tooltips
(the default is None)
Other Parameters
----------------
x : str, optional
alias of `time_column`
title : str, optional
Title to display (the default is None)
ref_event : Any, optional
Add a reference line/label using the alert time (the default is None)
ref_time : datetime, optional
Add a reference line/label using `ref_time` (the default is None)
group_by : str
(where `data` is a DataFrame)
The column to group timelines on
legend: str, optional
"left", "right", "inline" or "none"
(the default is to show a legend when plotting multiple series
and not to show one when plotting a single series)
yaxis : bool, optional
Whether to show the yaxis and labels
range_tool : bool, optional
Show the the range slider tool (default is True)
height : int, optional
The height of the plot figure
(the default is auto-calculated height)
width : int, optional
The width of the plot figure (the default is 900)
color : str
Default series color (default is "navy"). This is overridden by
automatic color assignments if plotting a grouped chart
kind : Union[str, List[str]]
one or more glyph types to plot., optional
Supported types are "circle", "line" and "vbar" (default is "vbar")
Returns
-------
figure
The bokeh plot figure.
"""
check_kwargs(kwargs, _DEFAULT_KWARGS + _TL_VALUE_KWARGS)
reset_output()
output_notebook()
height: int = kwargs.pop("height", None)
width: int = kwargs.pop("width", 900)
title: str = kwargs.pop("title", None)
time_column = kwargs.get("x", time_column)
group_by: str = kwargs.get("group_by", None)
show_yaxis: bool = kwargs.pop("yaxis", True)
show_range: bool = kwargs.pop("range_tool", True)
color: str = kwargs.get("color", "navy")
legend_pos: str = kwargs.pop("legend", None)
kind: Any = kwargs.pop("kind", ["vbar"])
plot_kinds = kind if isinstance(kind, list) else [kind]
ref_time, ref_label = _get_ref_event_time(**kwargs)
graph_df, group_count_df, tool_tip_columns, series_count = _create_data_grouping(
data, source_columns, time_column, group_by, color)
hover = HoverTool(
tooltips=_create_tool_tips(data, tool_tip_columns),
formatters={"Tooltip": "printf"},
)
# Create the Plot figure
title = title if title else "Timeline"
min_time = graph_df[time_column].min()
max_time = graph_df[time_column].max()
start_range = min_time - ((max_time - min_time) * 0.1)
end_range = max_time + ((max_time - min_time) * 0.1)
height = height if height else _calc_auto_plot_height(series_count)
plot = figure(
x_range=(start_range, end_range),
min_border_left=50,
plot_height=height,
plot_width=width,
x_axis_label="Event Time",
x_axis_type="datetime",
x_minor_ticks=10,
y_axis_label=y,
tools=[hover, "xwheel_zoom", "box_zoom", "reset", "save", "xpan"],
toolbar_location="above",
title=title,
)
plot.yaxis.visible = show_yaxis
plot.ygrid.minor_grid_line_color = "navy"
plot.ygrid.minor_grid_line_alpha = 0.1
plot.ygrid.grid_line_color = "navy"
plot.ygrid.grid_line_alpha = 0.3
plot.xgrid.minor_grid_line_color = "navy"
plot.xgrid.minor_grid_line_alpha = 0.1
plot.xgrid.grid_line_color = "navy"
plot.xgrid.grid_line_alpha = 0.3
# set the tick datetime formatter
plot.xaxis[0].formatter = _get_tick_formatter()
# plot groups individually so that we can create an interactive legend
if group_by:
legend_items = []
for _, group_id in group_count_df[group_by].items():
first_group_item = graph_df[graph_df[group_by] == group_id].iloc[0]
legend_label = str(first_group_item[group_by])
inline_legend = str(group_id) if legend_pos == "inline" else None
group_color = first_group_item["color"]
row_source = ColumnDataSource(
graph_df[graph_df[group_by] == group_id])
p_series = []
# create default plot args
plot_args: Dict[str, Any] = dict(
x=time_column,
alpha=0.7,
source=row_source,
legend_label=str(inline_legend),
)
if "vbar" in plot_kinds:
p_series.append(
plot.vbar(top=y, width=4, color="color", **plot_args))
if "circle" in plot_kinds:
p_series.append(
plot.circle(y=y, size=4, color="color", **plot_args))
if "line" in plot_kinds:
p_series.append(
plot.line(y=y,
line_width=1,
line_color=group_color,
**plot_args))
if not inline_legend:
legend_items.append((legend_label, p_series))
if legend_pos == "inline":
# Position the inline legend
plot.legend.location = "top_left"
plot.legend.click_policy = "hide"
elif legend_pos in ["left", "right"]:
# Create the legend box outside of the plot area
ext_legend = Legend(
items=legend_items,
location="center",
click_policy="hide",
label_text_font_size="8pt",
)
plot.add_layout(ext_legend, legend_pos)
else:
plot_args = dict(x=time_column,
color="color",
alpha=0.7,
source=ColumnDataSource(graph_df))
if "vbar" in plot_kinds:
plot.vbar(top=y, width=4, **plot_args)
if "circle" in plot_kinds:
plot.circle(y=y, size=4, **plot_args)
if "line" in plot_kinds:
plot.line(y=y, line_width=4, **plot_args)
# if we have a reference, plot the time as a line
if ref_time is not None:
_add_ref_line(plot, ref_time, ref_label, series_count)
if show_range:
rng_select = _create_range_tool(
data=graph_df,
min_time=min_time,
max_time=max_time,
plot_range=plot.x_range,
width=width,
height=height,
time_column=time_column,
)
show(column(plot, rng_select))
else:
show(plot)
return plot
# create a new plot (with a title) using figure
p = figure(
plot_width=400,
plot_height=400,
title="Comparison of Losses (in blue) and Validation Losses (in red)")
# add a line renderer
p.multi_line([
list(range(len(history.history["loss"]))),
list(range(len(history.history["val_loss"])))
], [history.history["loss"], history.history["val_loss"]],
color=["firebrick", "navy"],
line_width=2)
show(p) # show the results
# In[7]:
from sklearn.metrics import confusion_matrix
pred = model.predict(x_test)
pred = np.argmax(pred, axis=1)
y_test2 = np.argmax(y_test.values, axis=1)
# Compute confusion matrix
cm = confusion_matrix(y_test2, pred)
np.set_printoptions(precision=2)
print('Confusion matrix, without normalization')
#print(cm)