def test_silence_with_bad_input_and_check_warn(mock_warn: MagicMock, mock_error: MagicMock) -> None:
m = Mod(foo=-10)
with pytest.raises(ValueError, match="Input to silence should be a warning object"):
v.silence(cast(Any, "EXT:W"))
issues = v.check_integrity([m])
v.process_validation_issues(issues)
assert not mock_error.called
assert mock_warn.called
def test_silence_with_bad_input_and_check_warn(mock_warn, mock_error):
m = Mod(foo=-10)
with pytest.raises(ValueError,
match=('Input to silence should be a '
'warning object')):
v.silence('EXT:W')
v.check_integrity([m])
assert not mock_error.called
assert mock_warn.called
def silence_warnings(*warnings):
"""
Context manager for silencing bokeh validation warnings.
"""
for warning in warnings:
silence(warning)
try:
yield
finally:
for warning in warnings:
silence(warning, False)
def silence_warnings(*warnings):
"""
Context manager for silencing bokeh validation warnings.
"""
for warning in warnings:
silence(warning)
try:
yield
finally:
for warning in warnings:
silence(warning, False)
def test_silence_and_check_warn(mock_warn, mock_error):
from bokeh.core.validation.warnings import EXT
m = Mod(foo=-10)
try:
v.silence(EXT) # turn the warning off
v.check_integrity([m])
assert not mock_error.called
assert not mock_warn.called
finally:
v.silence(EXT, False) # turn the warning back on
v.check_integrity([m])
assert not mock_error.called
assert mock_warn.called
def test_silence_and_check_warn(mock_warn, mock_error) -> None:
from bokeh.core.validation.warnings import EXT
m = Mod(foo=-10)
try:
v.silence(EXT) # turn the warning off
issues = v.check_integrity([m])
v.process_validation_issues(issues)
assert not mock_error.called
assert not mock_warn.called
finally:
v.silence(EXT, False) # turn the warning back on
issues = v.check_integrity([m])
v.process_validation_issues(issues)
assert not mock_error.called
assert mock_warn.called
def test_silence_remove_warning_that_is_not_in_silencers_is_ok(
mock_warn, mock_error):
from bokeh.core.validation.warnings import EXT
m = Mod(foo=-10)
silencers0 = v.silence(EXT) # turn the warning off
assert len(silencers0) == 1
silencers1 = v.silence(EXT, False) # turn the warning back on
silencers2 = v.silence(EXT, False) # do it a second time - no-op
assert len(silencers1) == 0
assert silencers1 == silencers2
v.check_integrity([m])
assert not mock_error.called
assert mock_warn.called
def test_silence_warning_already_in_silencers_is_ok(mock_warn, mock_error):
from bokeh.core.validation.warnings import EXT
m = Mod(foo=-10)
try:
silencers0 = v.silence(EXT) # turn the warning off
silencers1 = v.silence(EXT) # do it a second time - no-op
assert len(silencers0) == 1
assert silencers0 == silencers1 # silencers is same as before
v.check_integrity([m])
assert not mock_error.called
assert not mock_warn.called
finally:
v.silence(EXT, False) # turn the warning back on
v.check_integrity([m])
assert not mock_error.called
assert mock_warn.called
from bokeh.io import output_file, show, save
from bokeh.layouts import column
from bokeh.plotting import figure
from bokeh.models import BoxAnnotation, Label, Range1d, WheelZoomTool, ResetTool, PanTool, LegendItem, Legend
from bokeh.core.validation.warnings import FIXED_SIZING_MODE
from bokeh.core.validation import silence
import easygui
from convert_fsa_to_csv import convert_folder
pd.set_option('display.max_columns', 20)
pd.set_option('display.width', 1000)
pd.set_option('display.max_rows', 50)
TOOLTIPS = [("(x,y)", "($x{1.1}, $y{int})")]
silence(FIXED_SIZING_MODE, True)
channels_of_interest = {
'IGH-A_channel_1': 'blue',
'IGH-B_channel_1': 'blue',
'IGH-C_channel_2': 'green',
'IGK-A_channel_1': 'blue',
'IGK-B_channel_1': 'blue',
'TCRB-A_channel_1': 'blue',
'TCRB-A_channel_2': 'green',
'TCRB-B_channel_1': 'blue',
'TCRB-C_channel_1': 'blue',
'TCRB-C_channel_2': 'green',
'TCRB-C_channel_3': 'orange',
'TCRG-A_channel_1': 'blue',
'TCRG-A_channel_2': 'green',
# /usr/bin/env python3
from bokeh.plotting import figure
from bokeh.models import LinearColorMapper, HoverTool, Div, ColorBar
from bokeh.tile_providers import get_provider
from bokeh.layouts import layout
from bokeh.io import curdoc
from bokeh.core.validation import silence
from bokeh.core.validation.warnings import MISSING_RENDERERS
from coordinate_transformation.to_web_merc import toWebMerc
from helper_functions.helper_funcs import hour_inputs, slider_input, \
source, update, button
# silence unnecessary warnings for color_bar_plot
silence(MISSING_RENDERERS, True)
# bokeh output HTML file
tile_provider = get_provider('CARTODBPOSITRON')
# base HTML web page for Bokeh visualization
homepage = Div(text=open('traffic_plot.html').read(), width=800)
# London longitude and latitude GPS coordinate range
london_x_range = (-0.25, 0.015)
london_y_range = (51.436, 51.568)
merc_lower_left = toWebMerc(london_x_range[0], london_y_range[0])
merc_upper_right = toWebMerc(london_x_range[1], london_y_range[1])
# tooltips on dats point hoverover
tooltips = [('Total traffic', '@sum_flux{0,0.00}'),
('Net flux', '@diff_flux{0,0.00}'),
from bokeh.plotting import *
from bokeh.models import ColumnDataSource, CustomJS, Slider, Button, DataTable, TableColumn
from bokeh.models import HoverTool, LinearColorMapper, NumberFormatter, RadioButtonGroup
from bokeh.models import Select, Spinner, RangeSlider, FileInput, MultiLine, PreText
from bokeh.models import Tabs, Panel, MultiSelect, RadioGroup, Div, LabelSet, Label
from bokeh import events
from bokeh.layouts import row, column, layout
from bokeh.io import curdoc, show
from bokeh.themes import Theme
from bokeh.core.validation import silence
from bokeh.core.validation.warnings import EMPTY_LAYOUT, MISSING_RENDERERS
from bokeh.palettes import Category20
# Ignore Warnings about Empty Plots on Initialization
silence(EMPTY_LAYOUT, True)
silence(MISSING_RENDERERS, True)
# Set the Output for the Bokeh Application
output_notebook()
### Define the Bokeh Application ###
# all code is inside this definition except for the call to show at the end #
def bkapp(doc):
### Functions ###
# functions for user dialogs
def open_file(ftype):
root = Tk()
def setupBokeh(self, cbase=None, clevels=None, creverse=None):
"""-----------------------------------------------------------------------------------------
SEt up four plot in 2 x 2 grid, but with differing sizes
mainplot is the dotplot itself, upper right
legend shows the colorbar legend
scoreplot shows the window score distribution
runploot shows the log of the run length distribution
:param cbase: string, e.g. Greys, Blues, Reds, Viridis, etc
:param clevels: int, usually 0-9 or 256
:param creverse: boolean, if True highest color is dark
:return: True
-----------------------------------------------------------------------------------------"""
# turn off MISSING_RENDERERS warning caused by plotting colorbars in empty plot
silence(MISSING_RENDERERS, True)
self.palette = self.setupPalette(cbase=cbase,
clevels=clevels,
creverse=creverse)
if self.title:
titlestr = self.title
else:
now = date.today()
titlestr = 'Dotplot of {} and {} - {}'.format(
self.s1.id, self.s2.id, now)
xlabel = '\n'.join([self.s1.id, self.s1.doc])
ylabel = '\n'.join([self.s2.doc, self.s2.id])
# account for sequence length difference, ylen scaling affects main and legend panels
xlen = 800
ylen = xlen * self.l2 / self.l1
# define each panel as a figure
label = '({}, {}, score)'.format(self.s1.id, self.s2.id)
TIPS = [(label, '($x{0}, $y{0}, @score)')]
self.figure['main'] = figure(title=titlestr,
x_axis_label=xlabel,
y_axis_label=ylabel,
height=int(ylen),
width=int(xlen),
align='center',
tooltips=TIPS)
self.figure['legend'] = figure(height=int(ylen), width=200)
TIPS = [('score, number', '$x{0}, $y{0.00}')]
self.figure['scoredist'] = figure(height=300, width=500, tooltips=TIPS)
TIPS = [('length,count', '$x{0}, $y{0}')]
self.figure['rundist'] = figure(height=300,
width=500,
y_axis_type='log',
tooltips=TIPS)
# grid layout
self.grid = layout([[self.figure['main'], self.figure['legend']],
[self.figure['scoredist'],
self.figure['rundist']]])
return True
def bokeh_plot(histo, jup_url="http://127.0.0.1:8889"):
if not isnotebook():
raise NotImplementedError("Only usable in jupyter notebook")
import bokeh.plotting.figure as bk_figure
from bokeh.io import curdoc, show
from bokeh import palettes
from bokeh.layouts import row, widgetbox, column
from bokeh.models import ColumnDataSource
from bokeh.models.widgets import RadioButtonGroup, CheckboxButtonGroup
from bokeh.models.widgets import RangeSlider, Div
from bokeh.io import output_notebook # enables plot interface in J notebook
import numpy as np
# init bokeh
from bokeh.application import Application
from bokeh.application.handlers import FunctionHandler
from bokeh.core.validation import silence
from bokeh.core.validation.warnings import EMPTY_LAYOUT
silence(EMPTY_LAYOUT, True)
output_notebook()
# Set up widgets
cfg_labels = ["Ghost"]
wi_config = CheckboxButtonGroup(labels=cfg_labels, active=[0])
wi_dense_select = RadioButtonGroup(
labels=[ax.name for ax in histo.dense_axes()], active=0)
wi_sparse_select = RadioButtonGroup(
labels=[ax.name for ax in histo.sparse_axes()], active=0)
# Dense widgets
sliders = {}
for ax in histo.dense_axes():
edge_vals = (histo.axis(ax.name).edges()[0],
histo.axis(ax.name).edges()[-1])
_smallest_bin = np.min(np.diff(histo.axis(ax.name).edges()))
sliders[ax.name] = RangeSlider(title=ax.name,
value=edge_vals,
start=edge_vals[0],
end=edge_vals[1],
step=_smallest_bin,
name=ax.name)
# Cat widgets
togglers = {}
for ax in histo.sparse_axes():
togglers[ax.name] = CheckboxButtonGroup(
labels=[i.name for i in ax.identifiers()],
active=[0],
name=ax.name)
# Toggles for all widgets
configers = {}
for ax in histo.sparse_axes():
configers[ax.name] = CheckboxButtonGroup(labels=["Display", "Ghost"],
active=[0, 1],
name=ax.name)
for ax in histo.dense_axes():
configers[ax.name] = CheckboxButtonGroup(labels=["Display"],
active=[0],
name=ax.name)
# Figure
fig = bk_figure(title="1D Projection",
plot_width=500,
plot_height=500,
min_border=20,
toolbar_location=None)
fig.yaxis.axis_label = "N"
fig.xaxis.axis_label = "Quantity"
# Iterate over possible overlays
_max_idents = 0 # Max number of simultaneou histograms
for ax in histo.sparse_axes():
_max_idents = max(_max_idents, len([i.name for i in ax.identifiers()]))
# Data source list
sources = []
sources_ghost = []
for i in range(_max_idents):
sources.append(
ColumnDataSource(dict(left=[], top=[], right=[], bottom=[])))
sources_ghost.append(
ColumnDataSource(dict(left=[], top=[], right=[], bottom=[])))
# Hist list
hists = []
hists_ghost = []
for i in range(_max_idents):
if _max_idents < 10:
_color = palettes.Category10[min(max(3, _max_idents), 10)][i]
else:
_color = palettes.magma(_max_idents)[i]
hists.append(
fig.quad(left="left",
right="right",
top="top",
bottom="bottom",
source=sources[i],
alpha=0.9,
color=_color))
hists_ghost.append(
fig.quad(left="left",
right="right",
top="top",
bottom="bottom",
source=sources_ghost[i],
alpha=0.05,
color=_color))
def update_data(attrname, old, new):
sparse_active = wi_sparse_select.active
sparse_name = [ax.name for ax in histo.sparse_axes()][sparse_active]
sparse_other = [
ax.name for ax in histo.sparse_axes() if ax.name != sparse_name
]
dense_active = wi_dense_select.active
dense_name = [ax.name for ax in histo.dense_axes()][dense_active]
dense_other = [
ax.name for ax in histo.dense_axes() if ax.name != dense_name
]
# Apply cuts in projections
_h = histo.copy()
for proj_ax in sparse_other:
_idents = histo.axis(proj_ax).identifiers()
_labels = [ident.name for ident in _idents]
if 0 in configers[proj_ax].active:
_h = _h.integrate(
proj_ax, [_labels[i] for i in togglers[proj_ax].active])
else:
_h = _h.integrate(proj_ax)
for proj_ax in dense_other:
_h = _h.integrate(
proj_ax,
slice(sliders[proj_ax].value[0], sliders[proj_ax].value[1]))
for cat_ix in range(_max_idents):
# Update histo for each toggled overlay
if cat_ix in togglers[sparse_name].active:
cat_value = histo.axis(sparse_name).identifiers()[cat_ix]
h1d = _h.integrate(sparse_name, cat_value)
# Get shown histogram
values = h1d.project(dense_name).values()
if values != {}:
h = values[()]
bins = h1d.axis(dense_name).edges()
# Apply cuts on shown axis
bin_los = bins[:-1][
bins[:-1] > sliders[dense_name].value[0]]
bin_his = bins[1:][bins[1:] < sliders[dense_name].value[1]]
new_bins = np.intersect1d(bin_los, bin_his)
bin_ixs = np.searchsorted(bins, new_bins)[:-1]
h = h[bin_ixs]
sources[cat_ix].data = dict(left=new_bins[:-1],
right=new_bins[1:],
top=h,
bottom=np.zeros_like(h))
else:
sources[cat_ix].data = dict(left=[],
right=[],
top=[],
bottom=[])
# Add ghosts
if 0 in wi_config.active:
h1d = histo.integrate(sparse_name, cat_value)
for proj_ax in sparse_other:
_idents = histo.axis(proj_ax).identifiers()
_labels = [ident.name for ident in _idents]
if 1 not in configers[proj_ax].active:
h1d = h1d.integrate(
proj_ax,
[_labels[i] for i in togglers[proj_ax].active])
else:
h1d = h1d.integrate(proj_ax)
values = h1d.project(dense_name).values()
if values != {}:
h = h1d.project(dense_name).values()[()]
bins = h1d.axis(dense_name).edges()
sources_ghost[cat_ix].data = dict(
left=bins[:-1],
right=bins[1:],
top=h,
bottom=np.zeros_like(h))
else:
sources_ghost[cat_ix].data = dict(left=[],
right=[],
top=[],
bottom=[])
else:
sources[cat_ix].data = dict(left=[],
right=[],
top=[],
bottom=[])
sources_ghost[cat_ix].data = dict(left=[],
right=[],
top=[],
bottom=[])
# Cosmetics
fig.xaxis.axis_label = dense_name
for name, slider in sliders.items():
slider.on_change('value', update_data)
for name, toggler in togglers.items():
toggler.on_change('active', update_data)
for name, configer in configers.items():
configer.on_change('active', update_data)
# Button
for w in [wi_dense_select, wi_sparse_select, wi_config]:
w.on_change('active', update_data)
from bokeh.models.widgets import Panel, Tabs
from bokeh.io import output_file, show
from bokeh.plotting import figure
layout = row(
fig,
column(
Div(text="<b>Overlay Axis:</b>",
style={
'font-size': '100%',
'color': 'black'
}), wi_sparse_select,
Div(text="<b>Plot Axis:</b>",
style={
'font-size': '100%',
'color': 'black'
}), wi_dense_select,
Div(text="<b>Categorical Cuts:</b>",
style={
'font-size': '100%',
'color': 'black'
}), *[toggler for name, toggler in togglers.items()],
Div(text="<b>Dense Cuts:</b>",
style={
'font-size': '100%',
'color': 'black'
}), *[slider for name, slider in sliders.items()]))
# Config prep
incl_lists = [[], [], []]
for i, key in enumerate(list(configers.keys())):
incl_lists[i // max(5,
len(list(configers.keys())) / 3)].append(
Div(text="<b>{}:</b>".format(key),
style={
'font-size': '70%',
'color': 'black'
}))
incl_lists[i // max(5,
len(list(configers.keys())) / 3)].append(
configers[key])
layout_cfgs = column(
row(
column(
Div(text="<b>Configs:</b>",
style={
'font-size': '100%',
'color': 'black'
}), wi_config)),
Div(text="<b>Axis togglers:</b>",
style={
'font-size': '100%',
'color': 'black'
}),
row(
column(incl_lists[0]),
column(incl_lists[1]),
column(incl_lists[2]),
))
# Update active buttons
def update_layout(attrname, old, new):
active_axes = [None]
for name, wi in configers.items():
if 0 in wi.active:
active_axes.append(name)
for child in layout.children[1].children:
if child.name not in active_axes:
child.visible = False
else:
child.visible = True
for name, configer in configers.items():
configer.on_change('active', update_layout)
tab1 = Panel(child=layout, title="Projection")
tab2 = Panel(child=layout_cfgs, title="Configs")
tabs = Tabs(tabs=[tab1, tab2])
def modify_doc(doc):
doc.add_root(row(tabs, width=800))
doc.title = "Sliders"
handler = FunctionHandler(modify_doc)
app = Application(handler)
show(app, notebook_url=jup_url)
update_data("", "", "")
import argparse # to easily parse arguments
import sys # sys.argv[1:] -- to obtain possible file path
from bokeh.server.server import Server
from bokeh.core import validation
import layout_factory as lf
import pandas as pd
validation.silence(1002, True) # silence the bokeh plot warnings
def hardwired_data():
x_name = 'Year, 1956 = 0'
y_name = 'Birds (sqrt)'
data_frame = pd.DataFrame()
data_frame[x_name] = [
0, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47
]
data_frame[y_name] = [
1.4142135623730951, 1.4142135623730951, 3.1622776601683795, 2.0,
3.1622776601683795, 3.4641016151377544, 3.1622776601683795,
2.8284271247461903, 4.123105625617661, 2.6457513110645907,
6.6332495807108, 7.0710678118654755, 5.0990195135927845,
3.1622776601683795, 2.6457513110645907, 1.0, 6.164414002968976,
9.591663046625438, 10.63014581273465, 9.0, 8.888194417315589,
8.48528137423857, 9.16515138991168, 8.18535277187245, 6.557438524302,
7.211102550927978, 8.18535277187245, 7.416198487095663,
# In[1]:
from bokeh.io import output_file, show, curdoc
from bokeh.plotting import figure
from bokeh.models import Div, Select, TextInput, BoxAnnotation, Toggle, ColumnDataSource, Label, LabelSet, Title
from bokeh.layouts import layout
from bokeh.resources import CDN
from bokeh.embed import file_html
from os.path import dirname, join
from bokeh.core.validation import silence
from bokeh.core.validation.warnings import EMPTY_LAYOUT
from bokeh.models.widgets import CheckboxGroup
# In[2]:
silence(EMPTY_LAYOUT, True)
# In[3]:
output_file("stacked.html", mode='inline')
# In[4]:
platform = [
'Nintendo DS', 'Playstation 2', 'Playstation 3', 'Nintendo Wii',
'Xbox 360', 'Playstation Portable', 'Playstation 1', 'PC',
'Game Boy Advance', 'Xbox', 'GameCube', 'Nintendo 3DS', 'Playstation 4',
'Playstation Vita', 'Nintendo 64', 'Super Nintendo', 'Xbox One',
'Sega Saturn', 'Nintendo WiiU', 'Atari 2600',
'Nintendo Entertainment System', 'Game Boy', 'Sega Dreamcast',
'Sega Genesis'
import sys
""" Class that imports TypeScript code for a custom tool: EnhanceTool
This tool lets the user create a rectangular selection area that specifies
a range of residue pairs to be displayed at a higher resolution.
(In other words, it takes the range of residues and redisplays the plot so
it shows only this range of residues at the given resolution. In this
way, it "enhances" the region.)
"""
class EnhanceTool(Tool):
__implementation__ = 'enhance_tool.ts'
source = Instance(ColumnDataSource)
validation.silence(MISSING_RENDERERS, True)
source = ColumnDataSource(data=dict(x=[], y=[]))
plot = figure(x_range=(0, 1),
y_range=(0, 1),
tools=[EnhanceTool(source=source)])
show(plot)
validation.silence(MISSING_RENDERERS, False)
""" Class that initiates and loops the Bokeh server
that houses a dashboard for the given plots
"""
class DashboardServer:
""" Initialization function
"""
def __init__(self,
