def edge_labels(graph_render):
source = graph_render.edge_renderer.data_source
xcoord = bkm.CustomJSTransform(v_func=EDGE_JS_CODE % "0",
args=dict(
provider=graph_render.layout_provider,
source=source))
ycoord = bkm.CustomJSTransform(v_func=EDGE_JS_CODE % "1",
args=dict(
provider=graph_render.layout_provider,
source=source))
source.data['labels'] = [
str(datum) if not pd.isnull(datum) else ''
for datum in source.data['relative_allocation']
]
# Use the transforms to supply coords to a LabelSet
labels = bkm.LabelSet(x=bkt.transform('start', xcoord),
y=bkt.transform('start', ycoord),
text='labels',
text_font_size="12px",
x_offset=0,
y_offset=0,
source=source,
render_mode='canvas')
return labels
def make_plot(source, df, title, title2):
plot = figure(x_axis_type="datetime",
plot_width=1500,
tools="",
toolbar_location="above")
plot.title.text = title
#plot.line("Date","ConfirmedCases",source=source)
plot.line("Date",
"PredictedDailyNewCases",
source=source,
line_width=3,
color="orange")
plot.line("Date", "DailyChangeConfirmedCases", source=source, line_width=3)
#plot.line(x=[current_time,current_time], y=[-10,50000], color="#FB8072", line_width=4, line_alpha =0.6, line_dash="dashed")
################### INTERVENTIONS #########################
colors = list(brewer['RdYlGn'][4])
colors[1] = '#FDE724'
colors[2] = '#FBA40A'
mapper = LinearColorMapper(palette=colors,
low=df["C1_School closing"].min(),
high=df["C2_Workplace closing"].max())
graph = figure(plot_width=1500,
plot_height=600,
title="Interventions",
x_range=dates,
y_range=interventions,
toolbar_location=None,
tools="",
x_axis_location=None)
for i, j in enumerate(interventions):
graph.rect(x="Date2",
y=i,
width=1.01,
height=0.8,
source=source,
line_color=transform(j, mapper),
fill_color=transform(j, mapper))
color_bar = ColorBar(color_mapper=mapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=len(colors)))
graph.add_layout(color_bar, 'right')
graph.axis.axis_line_color = None
graph.axis.major_tick_line_color = None
graph.axis.major_label_text_font_size = "10px"
graph.axis.major_label_standoff = 0
#graph.xaxis.major_label_orientation = 1.2
graph.outline_line_color = None
graph.xgrid.grid_line_color = None
#graph.line(x=[df["Date2"].iloc[-2],df["Date2"].iloc[-2]], y=["C1_School closing", "H6_Facial Coverings"], color="#FB8072", line_width=4, line_alpha =0.9, line_dash="dashed")
graph.title.text = title2
return plot, graph
def make_earning_plot(data, symbol=''):
num_of_year = len(data['year'].unique())
colors = magma(num_of_year)
mapper = LinearColorMapper(palette=colors,
low=data.year.max(),
high=data.year.min())
source = ColumnDataSource(data)
plot = figure(
x_range=Range1d(0, 5),
plot_height=500,
plot_width=1000,
)
reported = plot.circle(
x='quarter',
y='reported',
source=source,
name='reported',
legend='Reported',
size=20,
color=transform('year', mapper),
fill_color=transform('year', mapper),
)
estimated = plot.circle(
x='quarter',
y='estimate',
source=source,
name='estimated',
legend='Estimated',
size=15,
color=transform('year', mapper),
fill_alpha=0.4,
muted_alpha=0.1,
)
price_hover = HoverTool(renderers=[reported],
tooltips=[
("year: ", "@year"),
("reported: ", "@reported"),
("estimate: ", "@estimate"),
("surprise: ", "@surprise{0.2f}"),
("surprise_per: ", "@surprise_per"),
])
plot.add_tools(price_hover)
plot.title.text = f"{symbol.upper()} Earning" if symbol else "Earning"
plot.legend.location = "top_left"
plot.xaxis.axis_label = 'Quarter'
plot.yaxis.axis_label = 'Price'
plot.ygrid.band_fill_color = "olive"
plot.ygrid.band_fill_alpha = 0.1
plot.legend.click_policy = "mute"
plot.xaxis.ticker = [1, 2, 3, 4]
return plot
def setup_plot(src):
"""
Create the heatmap plot.
src: ColumnDataSource
"""
# Prepare a color pallete and color mapper
mapper = LinearColorMapper(
# force 0 to be mapped with white color
palette=tuple(
itertools.chain(["#FFFFFF"], tuple(reversed(Viridis256[1:])))),
low=0,
high=1000,
)
# Actual figure setup
p = figure(
plot_width=800,
plot_height=400,
x_range=(src.data["Miete"].min(), src.data["Miete"].max()),
y_range=(src.data["Einkommen"].min(), src.data["Einkommen"].max()),
tools="hover",
tooltips="Housing Benefit: @Wohngeld{0.0f}€",
)
p.rect(
x="Miete",
y="Einkommen",
width=25,
height=src.data["Einkommen"][1] - src.data["Einkommen"][0],
source=src,
line_color=transform("Wohngeld", mapper),
fill_color=transform("Wohngeld", mapper),
)
color_bar = ColorBar(
color_mapper=mapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=20),
formatter=NumeralTickFormatter(format="0€"),
label_standoff=12,
)
p.add_layout(color_bar, "right")
plot = plotstyle(p, plot_dict)
return plot
def render(pkg):
global current_rpm, level, hover, source
current_rpm = pkg
hist.append([pkg, level])
newG = Graph()
nrn, nre = graphe(pkg, newG)
if nrn == 0:
return Div(text="This package is unknown")
newgraph = from_networkx(newG, spring_layout, scale=4, center=(0, 0))
newplot = figure(title="RPM network",
sizing_mode="scale_width",
aspect_ratio=2,
x_range=(-2.2, 2.2),
y_range=(-2.1, 2.1),
tools="tap",
toolbar_location=None)
newplot.axis.visible = False
newplot.grid.visible = False
newgraph.node_renderer.glyph = Rect(height=0.07,
width=0.1,
fill_color="color",
fill_alpha=0.0,
line_alpha=0.0)
if nre != 0:
newgraph.edge_renderer.glyph = MultiLine(line_color="color",
line_alpha=0.8)
newplot.renderers.append(newgraph)
source = newgraph.node_renderer.data_source
xcoord = CustomJSTransform(v_func=code % "0",
args=dict(provider=newgraph.layout_provider))
ycoord = CustomJSTransform(v_func=code % "1",
args=dict(provider=newgraph.layout_provider))
source.selected.on_change('indices', selected)
labels = LabelSet(x=transform('index', xcoord),
y=transform('index', ycoord),
text='name',
text_font_size="12px",
y_offset=-6,
x_offset="offset",
background_fill_color='color',
background_fill_alpha=0.85,
border_line_color='color',
border_line_alpha=1.0,
source=source,
render_mode='canvas')
newplot.add_tools(hover)
newplot.add_layout(labels)
return newplot
def update_plot(attr, old, new):
length = slider.value
width = slider.value
new_df = get_dataset(length, width)
source.data.update(new_df.data)
plot.x_range.factors = [str(x) for x in list(range(1, length + 1))]
plot.y_range.factors = [str(x) for x in list(range(1, width + 1))]
plot.image_url(url=['myapp/static/images/sh1.jpg'],
x=0,
y=0,
w=length,
h=length,
anchor="bottom_left")
colors = [
"#550b1d", "#933b41", "#cc7878", "#ddb7b1", "#dfccce", "#e2e2e2",
"#c9d9d3", "#a5bab7", "#75968f"
]
mapper = LinearColorMapper(palette=colors, low=0, high=100)
plot.rect(x="length",
y="width",
width=1,
height=1,
source=source,
line_color=None,
fill_color=transform('score', mapper),
alpha=0.4)
hover = HoverTool(tooltips=[("Potential Score for District Energy System",
"@score")])
plot.add_tools(hover)
p.text = "<h><b>The Shanghai city has been evaluated by %d districts for tessellation</b></h>" % (
length * width)
def make_correlation_plot(df, param_list):
df_corr = df[param_list].corr().fillna(0)
df_corr = df_corr.stack().rename("value").reset_index()
print(df_corr)
colors = RdBu[11]
# Had a specific mapper to map color with value
mapper = LinearColorMapper(palette=colors, low=-1, high=1)
corr_figure.x_range.factors = list(df_corr.level_0.drop_duplicates())
corr_figure.y_range.factors = list(df_corr.level_1.drop_duplicates())
hover = HoverTool(tooltips=[
("Corr", "@value"),
])
# Create rectangle for heatmap
corr_figure.rect(x="level_0",
y="level_1",
width=1,
height=1,
source=ColumnDataSource(df_corr),
line_color=None,
fill_color=transform('value', mapper))
corr_figure.add_tools(hover)
# Add legend
color_bar = ColorBar(color_mapper=mapper, location=(0, 0))
corr_figure.add_layout(color_bar, 'left')
def heatmap():
data=pd.DataFrame(
[ [1,0.2,0.3],
[0.3,1,0.5],
[-0.5,0.8,1]],
columns=['a','b','c'])
value=[]
for x in data.apply(tuple):
value.extend(x)
absValue=[abs(number) for number in value]
print(data)
source={
'x': [i for i in list(data.columns) for j in list(data.columns)],
'y': list(data.columns)*len(data.columns),
'value':value,
'abs':absValue
}
p=figure(title = "heatmap", sizing_mode="fixed", plot_width=600, plot_height=400,tools='pan,wheel_zoom,box_zoom,save,reset',x_range=list(data.columns),y_range=list(reversed(data.columns)))
p.toolbar.logo=None
from bokeh.models import LinearColorMapper
from bokeh.palettes import inferno,YlOrRd,Magma,PuBu,Greys
from bokeh.transform import transform
crs=PuBu[9]
crs.reverse()
mapper = LinearColorMapper(palette=crs, low=min(absValue), high=max(absValue))
fontMapper=LinearColorMapper(palette=[Greys[5][0],Greys[5][4]], low=min(absValue), high=max(absValue))
p.rect(x="x", y="y", width=1, height=1, source=source,
line_color=None, fill_color=transform('abs', mapper))
p.text(x="x", y="y",text='value', source=source,text_font_size='2em',text_font_style='bold',text_align='center',text_baseline='middle',text_color=transform('abs',fontMapper))
p.add_tools(
HoverTool(tooltips = [('Value', '@value')])
)
return json.dumps(json_item(p))
def draw(self, size=400):
index_label = 'Predicted'
column_label = 'Actual'
matrix = self.generate_data()
min_val, max_val = matrix.Value.min(), matrix.Value.max()
source = ColumnDataSource(matrix)
mapper = LinearColorMapper(palette=COLORS, low=min_val, high=max_val)
hover = HoverTool(tooltips=[
('Number', f"@Value")
])
p = figure(plot_width=size,
plot_height=size,
title='Confusion Matrix',
tools=[hover],
toolbar_location=None,
x_range=self.labels,
y_range=list(reversed(self.labels)))
p.yaxis.axis_label = index_label
p.xaxis.axis_label = column_label
p.rect(x=column_label,
y=index_label,
width=1,
height=1,
source=source,
fill_color=transform('Value', mapper))
self.plot = p
return p
def make_plot(mapper_type, palette):
mapper_opts = dict(palette=palette, low=1, high=1000)
if mapper_type == "linear":
mapper = LinearColorMapper(**mapper_opts)
else:
mapper = LogColorMapper(**mapper_opts)
p = figure(toolbar_location=None,
tools='',
title="",
x_axis_type=mapper_type,
x_range=(1, 1000))
p.title.text = f"{palette} with {mapper_type} mapping"
p.circle(x='x',
y='y',
alpha=0.8,
source=source,
size=6,
fill_color=transform('x', mapper),
line_color=None)
color_bar = ColorBar(color_mapper=mapper,
ticker=p.xaxis.ticker,
formatter=p.xaxis.formatter,
padding=0)
p.add_layout(color_bar, 'below')
return p
def createMatrix(width, height, column_list_original, index_list_original, mapper, color_bar, source_normal):
#Color mapper
#Hover information
hover = HoverTool()
hover.tooltips = [
("(Author1, Author2)", "(@AuthorX, @AuthorY)"),
("Similarity rate", "@sim"),
("Index", "@index")
]
#Basic interaction tools
TOOLS = "save,pan,box_zoom,reset,wheel_zoom"
#Graph grid and properties
figure_matrix = figure(plot_width = width, plot_height=height,
x_range=column_list_original, y_range=index_list_original, #feeding columns and range
toolbar_location="right", tools=TOOLS, x_axis_location="above")
r = figure_matrix.rect(x='AuthorX', y='AuthorY', width=1, height=1, source=source_normal,#feeding x,y for each square
line_color=None, fill_color=transform('sim', mapper))
figure_matrix.tools.append(hover)
figure_matrix.add_layout(color_bar, 'right')
figure_matrix.axis.axis_line_color = None
figure_matrix.axis.major_tick_line_color = None
figure_matrix.axis.major_label_text_font_size = "7pt"
figure_matrix.axis.major_label_standoff = 0
figure_matrix.xaxis.major_label_orientation = np.pi/2
return figure_matrix
def create_corrplot(df, timeframe, mpr, wd):
df = df.pct_change()
df = df.corr()
df.index.name = 'allcurrenciesX'
df.columns.name = 'allcurrenciesY'
#formatting the dataframe
df = df.stack().rename("value").reset_index()
#mapper = LinearColorMapper( palette=PuBu[9], low=0, high=1)
Hover = HoverTool(tooltips=[
('corr-coefficient', '@value'),
], )
toolstoadd = "box_zoom", "reset"
p = figure(tools=toolstoadd,
plot_width=wd,
plot_height=400,
title="Correlation plot for " + timeframe + " period",
x_range=list(df.allcurrenciesX.drop_duplicates()),
y_range=list(df.allcurrenciesY.drop_duplicates()),
toolbar_location="above",
x_axis_location="below")
p.add_tools(Hover)
p.rect(x="allcurrenciesX",
y="allcurrenciesY",
width=1,
height=1,
source=ColumnDataSource(df),
line_color=None,
fill_color=transform('value', mpr))
return p
def cm_callback():
global target_data
cm = confusion_matrix(target_data[label_select.value],
target_data[pred_select.value])
cm = pd.DataFrame(cm)
cm = cm.stack().reset_index().rename(
columns={
'level_0': label_select.value,
'level_1': pred_select.value,
0: 'count'
})
confusion_matrix_source.data = cm
mapper = LinearColorMapper(palette=Viridis256,
low=cm['count'].min(),
high=cm['count'].max())
hm.rect(x=pred_select.value,
y=label_select.value,
source=confusion_matrix_source,
width=1,
height=1,
line_color=None,
fill_color=transform('count', mapper))
hm.text(x=pred_select.value,
y=label_select.value,
text="count",
text_font_style="bold",
source=confusion_matrix_source,
text_align="left",
text_baseline="middle")
color_bar = ColorBar(color_mapper=mapper, label_standoff=12)
hm.add_layout(color_bar, 'right')
hm.visible = True
unvisible_other_plots(hm, visible_plots)
def create_marauder_map_figure(mdate):
df = RIndexStock().get_data(mdate)
TOOLTIPS = [("code", "@code"), ("(pday, profit)", "(@pday, @profit)")]
TOOLS = [BoxZoomTool(), ResetTool(), HoverTool(tooltips=TOOLTIPS)]
p = figure(x_axis_label='时间',
y_axis_label='强度',
tools=TOOLS,
toolbar_location="above",
title="牛熊比例")
if df is None or df.empty: return p
source = ColumnDataSource(df)
color_mapper = LinearColorMapper(palette="Viridis256",
low=df.profit.min(),
high=df.profit.max())
p.circle(x='pday',
y='profit',
color=transform('profit', color_mapper),
size=5,
alpha=0.6,
source=source)
color_bar = ColorBar(color_mapper=color_mapper,
label_standoff=12,
location=(0, 0),
title='强度')
p.add_layout(color_bar, 'right')
return p
def _bokeh_heatmap(source,
colormapper,
x_label,
y_label,
x_range,
y_range,
x_log=False,
y_log=False):
p = figure(x_range=x_range,
y_range=y_range,
x_axis_type="log" if x_log else "linear",
y_axis_type="log" if y_log else "linear",
toolbar_location=None,
tools="")
p.rect(x=x_label,
y=y_label,
width=1,
height=1,
source=source,
fill_color=transform('zz', colormapper),
line_color=None)
color_bar = ColorBar(color_mapper=colormapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=20),
formatter=BasicTickFormatter(use_scientific=False))
p.add_layout(color_bar, 'right')
p.xaxis.axis_label = x_label
p.yaxis.axis_label = y_label
return p
def two_station_heatmap(self):
fig = figure(width=700, match_aspect=True, tools='')
fig.xgrid.grid_line_color = None
fig.ygrid.grid_line_color = None
s_id1, s_id2 = self.x_select.value, self.y_select.value
df_counts = self.df_bikes_avail.groupby(
[s_id1, s_id2]).size().reset_index(name='counts')
df_counts.rename(columns={s_id1: s_id1, s_id2: s_id2}, inplace=True)
source = ColumnDataSource(df_counts)
pallette = [
'#084594', '#2171b5', '#4292c6', '#6baed6', '#9ecae1', '#c6dbef',
'#deebf7', '#f7fbff'
][::-1]
mapper = LinearColorMapper(palette=pallette,
low=0,
high=df_counts.counts.max())
color_bar = ColorBar(color_mapper=mapper)
fig.rect(x=str(s_id1),
y=str(s_id2),
width=1.0,
height=1.0,
line_alpha=0.0,
fill_color=transform('counts', mapper),
source=source)
fig.add_layout(color_bar, 'right')
return fig
def plot_heatmap_condition(condition2plot):
""" Create heatmap plot: x axis = time, y axis = MSOAs, colour = nr people with condition = condition2plot. condition2plot is key to conditions_dict."""
# Prep data
var2plot = msoacounts_dict[condition2plot]
var2plot = var2plot.rename_axis(None, axis=1).rename_axis('MSOA', axis=0)
var2plot.columns.name = 'Day'
# reshape to 1D array or rates with a month and year for each row.
df_var2plot = pd.DataFrame(var2plot.stack(), columns=['condition']).reset_index()
source = ColumnDataSource(df_var2plot)
# add better colour
mapper_1 = LinearColorMapper(palette=colours_ch_cond[condition2plot], low=0, high=var2plot.max().max())
# create fig
s1 = figure(title="Heatmap",
x_range=list(var2plot.columns), y_range=list(var2plot.index), x_axis_location="above")
s1.rect(x="Day", y="MSOA", width=1, height=1, source=source,
line_color=None, fill_color=transform('condition', mapper_1))
color_bar_1 = ColorBar(color_mapper=mapper_1, location=(0, 0), orientation = 'horizontal', ticker=BasicTicker(desired_num_ticks=len(colours_ch_cond[condition2plot])))
s1.add_layout(color_bar_1, 'below')
s1.axis.axis_line_color = None
s1.axis.major_tick_line_color = None
s1.axis.major_label_text_font_size = "7px"
s1.axis.major_label_standoff = 0
s1.xaxis.major_label_orientation = 1.0
# Create hover tool
s1.add_tools(HoverTool(
tooltips=[
( f'Nr {condition2plot}', '@condition'),
( 'Day', '@Day' ),
( 'MSOA', '@MSOA'),
],
))
s1.toolbar.autohide = False
plotref_dict[f"hm{condition2plot}"] = s1
def _plot_wcorr(Wcorr, L):
f = figure(tools="box_select, pan, reset, save")
f.plot_width = 700
f.plot_height = 600
# Background settings
f.background_fill_color = '#859dcd'
f.background_fill_alpha = 0.05
# Title settings
f.title.text = "W-Correlation for L={}".format(L)
f.title.text_font = 'Helvetica'
f.title.text_font_size = '24px'
f.title.align = 'center'
f.title.text_font_style = "italic"
# Axis settings
f.xaxis.axis_label = 'Fⱼ'
f.yaxis.axis_label = 'Fᵢ'
f.axis.axis_label_text_font = 'Helvetica'
f.axis.axis_label_text_font_size = '24px'
f.axis.major_label_orientation = 0
f.x_range = Range1d(start=0.5, end=L + 0.5)
f.y_range = Range1d(start=L + 0.5, end=0.5)
f.axis[0].ticker.desired_num_ticks = L
f.axis[0].ticker.num_minor_ticks = 0
data = DataFrame(Wcorr)
axis = [i for i in range(1, Wcorr.shape[0] + 1)]
data['F_i'] = axis
data.set_index('F_i', inplace=True)
data.columns = axis
data.columns.name = 'F_j'
df = DataFrame(data.stack(), columns=['corr']).reset_index()
source = ColumnDataSource(df)
# this is the colormap from the original NYTimes plot
mapper = LinearColorMapper(palette=color.palettes['colors_2'], low=0, high=1)
f.rect(x="F_i", y="F_j", width=1, height=1, source=source,
line_color=None, fill_color=transform('corr', mapper))
color_bar = ColorBar(color_mapper=mapper, location=(0, 0),
ticker=BasicTicker(desired_num_ticks=len(color.palettes['colors_2'])),
formatter=PrintfTickFormatter(format="%.2f"))
f.add_layout(color_bar, 'right')
hover = HoverTool(tooltips=[("Components", "(@F_i, @F_j)"),
("Correlations", "@corr")])
f.add_tools(hover)
show(f)
def mat(self, output_name, nodesX, nodesY, counts):
xname = []
yname = []
for node1 in nodesX:
for node2 in nodesY:
xname.append(node1)
yname.append(node2)
source = ColumnDataSource(data=dict(
xnames=xname,
ynames=yname,
count=counts.flatten(),
))
colors = ["#FFFFFF", "#CCCCFF", "#9999FF", "#5555FF", "#0000FF", "#0000CC", "#0000AA", "#000088", "#000000"]
exp_cmap = LogColorMapper(palette=colors, low = 0, high = 10)
# exp_cmap = LogColorMapper(palette=colors, low = np.min(counts), high = np.max(counts))
p = figure(title="Matrix Figure",
x_axis_location="above", tools="hover,save",
x_range=nodesX, y_range=list(reversed(nodesY)))
p.rect(x='xnames', y='ynames', width=0.9, height=0.9,
source=source, line_color=None, fill_color=transform('count', exp_cmap))
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
#圖例
color_bar = ColorBar(color_mapper=exp_cmap, location=(0, 0),
ticker=BasicTicker(desired_num_ticks=len(colors)),
formatter=PrintfTickFormatter(format="%d"))
p.add_layout(color_bar, 'right')
#游標所指“點”的說明格式
p.select_one(HoverTool).tooltips = [
('names', '@ynames -> @xnames'),
('count', '@count'),
]
output_file(output_name + ".html", title=output_name)
show(p) # show the plot
def node_labels(graph_render):
source = graph_render.node_renderer.data_source
xcoord = bkm.CustomJSTransform(
v_func=NODE_JS_CODE % "0",
args=dict(provider=graph_render.layout_provider))
ycoord = bkm.CustomJSTransform(
v_func=NODE_JS_CODE % "1",
args=dict(provider=graph_render.layout_provider))
# Use the transforms to supply coords to a LabelSet
labels = bkm.LabelSet(x=bkt.transform('index', xcoord),
y=bkt.transform('index', ycoord),
text='index',
text_font_size="10px",
x_offset=0,
y_offset=-5,
source=source,
render_mode='canvas',
text_align='center')
return labels
def heatmap(x=None,
y=None,
z=None,
data=None,
x_order=None,
y_order=None,
p=None,
width=1200,
height=500,
**plot_kw):
if x_order is None:
x_order = data[x[0]].unique()
if y_order is None:
y_order = data[y].unique()
tooltips = zip(data.columns, '@' + data.columns)
if p is None:
p = figure(height=max(height, 10 * len(y_order)),
plot_width=max(width, 10 * len(x_order)),
tooltips=list(tooltips),
tools=CFG['tools'],
x_range=x_order.tolist(),
y_range=y_order.tolist(),
x_axis_location="above",
min_border=CFG['padding'])
mapper = LinearColorMapper(palette=cc.fire,
low=data[z].min(),
high=data[z].max())
p.rect(x=x[0],
y=y,
width=1,
height=1,
source=data,
line_color=None,
fill_color=transform(z, mapper))
color_bar = ColorBar(color_mapper=mapper,
ticker=BasicTicker(desired_num_ticks=5),
location=(0, 0))
p.add_layout(color_bar, 'right')
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_text_font_size = "8pt"
p.axis.major_label_standoff = 0
p.xaxis.major_label_orientation = 'vertical'
return p
def general_mapper(column, mapped_to, to_map):
m = dict(zip(to_map, mapped_to))
v_func = """
const first = xs[0]
const norm = new Float64Array(xs.length)
for (let i = 0; i < xs.length; i++) {
norm[i] = m[xs[i]];
}
return norm
"""
t = CustomJSTransform(args={"m": m}, v_func=v_func)
return transform(column, t)
def matrix_heatmap(the_matrix):
'Create a bokeh graphic with matrix cells colored by value. Or use bokeh "heatmap".'
# pandas 'stack' is equivalent to R reshape gather, or melt from reshape2, from wide to long format.
# Prepare data.frame in the right format
# the_matrix.drop(['F', 'sup'], axis=1, inplace=True)
# the_matrix.columns= the_matrix.index
df = the_matrix.stack().rename("value").reset_index()
# The plot output:
# output_file(ROOT_DIR / "cmPlot.html")
# You can use your own palette here
colors = brewer['YlGnBu'][9][1:9]
# Had a specific mapper to map color with value
mapper = LinearColorMapper(
palette=colors, low=df.value.min(), high=df.value.max())
# Define a figure
p = figure(
plot_width=800,
plot_height=700,
title="20 Newsgroups Confusion Matrix",
y_range=list(df.level_0.drop_duplicates()),
x_range=list(df.level_1.drop_duplicates()),
toolbar_location=None,
tools="",
x_axis_location="above")
df['cnt'] = df['value'].apply(str)
cds = ColumnDataSource(df)
# Create rectangle for heatmap
p.rect(
y="level_0",
x="level_1",
alpha = 0.4,
width=1,
height=1,
source=cds,
line_color=None,
fill_color=transform('value', mapper))
glyph = Text(y="level_0", x="level_1", text="cnt", x_offset= -10.0, y_offset=10.0, text_color="black")
p.add_glyph(cds, glyph)
#Add legend
color_bar = ColorBar(
color_mapper=mapper,
location=(0,0),
ticker=BasicTicker(desired_num_ticks=len(colors)))
p.add_layout(color_bar, 'right')
return p
def plotConfusionMatrix(df, width, height):
from bokeh.palettes import Blues8
# Had a specific mapper to map color with value
mapper = LinearColorMapper(palette=Blues8[::-1],
low=df.value.min(),
high=df.value.max())
TOOLS = "hover,save,reset"
# Define a figure
p = figure(
plot_width=width,
plot_height=height,
# title="",
x_range=list(df.Treatment.drop_duplicates()),
y_range=list(df.Prediction.drop_duplicates()),
toolbar_location='above',
tools=TOOLS,
tooltips=[('Counts', '@value')],
x_axis_location="below")
p.xaxis.axis_label = "Prediction"
p.yaxis.axis_label = "Truth"
# Create rectangle for heatmap
p.rect(x="Prediction",
y="Treatment",
width=1,
height=1,
source=ColumnDataSource(df),
line_color=None,
fill_color=transform('value', mapper))
# Add legend
color_bar = ColorBar(color_mapper=mapper,
location=(0, 0),
label_standoff=12,
border_line_color=None,
ticker=BasicTicker(desired_num_ticks=len(Blues8)))
color_bar.background_fill_alpha = 0.0
p.add_layout(color_bar, 'right')
p.background_fill_alpha = 0.0
p.border_fill_alpha = 0.0
return p
def create_confusion_matrix(results_df, pred_column, logger):
y_true = results_df['Orig_Label'].values
crt_y_pred = results_df[pred_column].values
num_classes = int(logger.config_dict['NUM_CLASSES'])
cmat = confusion_matrix(y_true, crt_y_pred)
df = pd.DataFrame(cmat,
columns=[str(i) for i in range(num_classes)],
index=[str(i) for i in range(num_classes)])
df.index.name = 'Label'
df.columns.name = 'Prediction'
df = df.stack().rename("value").reset_index()
colors = [matplotlib.colors.rgb2hex(c) for c in sns.color_palette("Blues")]
mapper = LinearColorMapper(palette=colors,
low=df.value.min(),
high=df.value.max())
p = figure(plot_width=800,
plot_height=800,
title="Confusion matrix for {} test data".format(pred_column),
x_range=list(df.Label.drop_duplicates()),
y_range=list(df.Prediction.drop_duplicates()),
tools="wheel_zoom,box_zoom,save, hover")
p.rect(x="Label",
y="Prediction",
width=1,
height=1,
source=ColumnDataSource(df),
line_color=None,
fill_color=transform('value', mapper))
color_bar = ColorBar(color_mapper=mapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=len(colors)))
hover = p.select(dict(type=HoverTool))
hover.tooltips = [("Value", "@value"), ("Label", "@Label"),
("Prediction", "@Prediction")]
p.add_layout(color_bar, 'right')
model_type = logger.config_dict['RESULTS_FILE'].split('_')[0]
output_file(
logger.get_output_file("{}_{}_cmat.html".format(
model_type, pred_column)))
save(p)
return df
def viz_dist_map(df):
#df = df.loc[df['station']]
df = df.loc[(df['week'] >= 2) & (df['week'] <= 29)]
df.station = df.station.astype('str')
df['unique_day'] = df.apply(lambda x: 'w{}d{}'.format(x['week'], x['day']),
axis=1)
df.unique_day = df.unique_day.astype('str')
df = df.drop(columns=['year', 'week', 'day', 'satsun', 'counts'])
df = df.set_index('unique_day').reset_index()
source = ColumnDataSource(df)
mapper = LinearColorMapper(palette=brewer['PRGn'][11],
low=-0.05,
high=1.05)
print(list(df.percentile))
p = figure(plot_width=1000,
plot_height=800,
x_range=list(df.unique_day.unique()),
y_range=list(df.station.unique()),
toolbar_location='above',
x_axis_location="above")
p.rect(y="station",
x="unique_day",
width=1,
height=1,
source=source,
line_color=None,
fill_color=transform('percentile', mapper))
color_bar = ColorBar(
color_mapper=mapper,
location=(0, 0),
ticker=FixedTicker(
ticks=[0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.95
]),
label_standoff=5,
orientation='horizontal')
p.add_layout(color_bar, 'below')
p.xaxis.major_label_text_color = None
p.yaxis.major_label_text_color = None
p.add_tools(
HoverTool(tooltips=[('station', '@station'), ('day', '@unique_day')]))
return p
def plot_wordsAwards(df,
amount_awarded_per_day,
word_count,
y_axis_type='log',
title='Funding vs Number of words used in the abstract'):
wm = df[[amount_awarded_per_day, word_count]]
source = ColumnDataSource(wm)
color_mapper = LinearColorMapper(palette="Viridis256",
low=wm['amount_awarded_per_day'].min(),
high=wm['amount_awarded_per_day'].max())
p = figure(plot_width=1000,
plot_height=450,
tools='box_select, wheel_zoom, reset, save',
toolbar_location='above',
x_axis_label='word count',
y_axis_label='amount awarded per day (log)',
y_axis_type=y_axis_type)
p.circle(x=word_count,
y=amount_awarded_per_day,
color=transform(amount_awarded_per_day, color_mapper),
size=10,
alpha=0.6,
source=wm)
p.title.text = title
color_bar = ColorBar(color_mapper=color_mapper,
label_standoff=15,
location=(0, 0),
title='Amount awarded per day')
p.add_layout(color_bar, 'right')
p.title.text_font_size = "16pt"
p.title.text_color = 'MidnightBlue'
p.xaxis.axis_label_text_font_size = '15pt'
p.yaxis.axis_label_text_font_size = '15pt'
# export plots
_ = export_png(p, filename=img_path / 'wordawards.png')
#output_file(img_path/'file.html')
#p.output_backend = "svg"
#export_svgs(p, filename=img_path/"file.svg")
#display plot
show(p)
def viewCorr(self, nugget):
# Read Nugget to DataFrame
nfile = self.nuggetDataPath + nugget + '.pkl'
df = pd.read_pickle(nfile)
# Get info from Nugget filename
info = self.nugInfo(nfile)
# Attach theme to current document
curdoc().theme = self.bokehTheme # light_minimal dark_minimal
# Now we will create correlation matrix using pandas
df = df.iloc[:, 0:-6]
df = df.corr()
# Rename index and columns
df.index.name = 'AllColumns1'
df.columns.name = 'AllColumns2'
# Prepare data.frame in the right format
df = df.stack().rename("value").reset_index()
# You can use your own palette here
# colors = ['#d7191c', '#fdae61', '#ffffbf', '#a6d96a', '#1a9641']
# I am using 'Viridis256' to map colors with value, change it with 'colors' if you need some specific colors
mapper = LinearColorMapper(
palette=Viridis256, low=df.value.min(), high=df.value.max())
# Define a figure and tools
TOOLS = "pan,wheel_zoom,box_zoom,reset"
p = figure(
tools=TOOLS,
sizing_mode='scale_width',
title="Correlation plot of " + info['symb'] + ' ' + info['timeframe'],
x_range=list(df.AllColumns1.drop_duplicates()),
y_range=list(df.AllColumns2.drop_duplicates()),
toolbar_location="right",
x_axis_location="below")
# Create rectangle for heatmap
p.rect(
x="AllColumns1",
y="AllColumns2",
width=1,
height=1,
source=ColumnDataSource(df),
line_color=None,
fill_color=transform('value', mapper))
# Add legend
color_bar = ColorBar(
color_mapper=mapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=10))
p.xaxis.major_label_orientation = pi / 4
p.add_layout(color_bar, 'right')
return components(p)
def update(attr, old, new):
boroughs_to_plot = [
borough_selection.labels[i] for i in borough_selection.active
]
if isinstance(date_range_slider.value[0], (int, float)):
start_date = pd.Timestamp(float(date_range_slider.value[0]) * 1e6)
end_date = pd.Timestamp(float(date_range_slider.value[1]) * 1e6)
else:
start_date = pd.Timestamp(date_range_slider.value[0])
end_date = pd.Timestamp(date_range_slider.value[1])
new_src = make_dataset(x, y, boroughs_to_plot, start_date, end_date)
src.data.update(new_src.data)
print('plotting new stuff')
colors = [
"#4f685f", '#64827c', "#75968f", "#a5bab7", "#c9d9d3", "#e2e2e2",
"#f9eed4", "#f9d1ac", "#ddb7b1", "#cc7878", "#a54c4c", "#933b41",
"#550b1d"
]
mapper = LinearColorMapper(palette='Magma256',
low=src.data['value'].min(),
high=src.data['value'].max())
if x_ticks:
x_range = x_ticks
else:
x_range = sorted(list(set(src.data['x'])))
if y_ticks:
y_range = y_ticks
else:
y_range = sorted(list(set(src.data['y'])))
p = figure(plot_width=1100,
plot_height=700,
x_range=x_range,
y_range=y_range,
title=title)
p.rect(x='x',
y='y',
width=1,
height=1,
source=src,
line_color='white',
fill_color=transform('value', mapper))
color_bar = ColorBar(color_mapper=mapper,
location=(0, 0),
ticker=BasicTicker(desired_num_ticks=len(colors)))
p.add_layout(color_bar, 'right')
print('new stuff done')
def get_moonplot(exposures,
width=250,
height=250,
min_border_left=50,
min_border_right=50):
'''
Generates a scatter plot of MOONFRAC vs MOONALT. Each point is then colored
with a gradient corresponding to its MOONSEP.
Args:
exposures: Table of exposures with columns "MOONFRAC", "MOONALT", "MOONSEP"
Options:
width, height: plot width and height in pixels
min_border_left, min_border_right: set minimum width for external labels in pixels
Returns bokeh Figure object
'''
p = bk.figure(plot_width=width,
plot_height=height,
x_axis_label="Moon Fraction",
y_axis_label="Moon Altitude",
min_border_left=min_border_left,
min_border_right=min_border_right)
keep = exposures['PROGRAM'] != 'CALIB'
exposures_nocalib = exposures[keep]
color_mapper = LinearColorMapper(palette="Magma256", low=0, high=180)
source = ColumnDataSource(data=dict(MOONFRAC=exposures_nocalib["MOONFRAC"],
MOONALT=exposures_nocalib["MOONALT"],
MOONSEP=exposures_nocalib["MOONSEP"]))
color_bar = ColorBar(color_mapper=color_mapper,
label_standoff=12,
location=(0, 0),
width=5)
p.add_layout(color_bar, 'right')
p.title.text = 'Moon Fraction vs Moon Altitude, colored with MOONSEP'
p.circle("MOONFRAC",
"MOONALT",
color=transform('MOONSEP', color_mapper),
alpha=0.5,
source=source)
return p
cmap = LinearColorMapper(palette=Viridis11, low=min(unemployment.values()), high=max(unemployment.values()))
county_source = ColumnDataSource(
data=dict(
county_xs=[us_counties[code]["lons"] for code in us_counties if us_counties[code]["state"] not in ["ak", "hi", "pr", "gu", "vi", "mp", "as"]],
county_ys=[us_counties[code]["lats"] for code in us_counties if us_counties[code]["state"] not in ["ak", "hi", "pr", "gu", "vi", "mp", "as"]],
rate=[unemployment[code] for code in us_counties if us_counties[code]["state"] not in ["ak", "hi", "pr", "gu", "vi", "mp", "as"]],
)
)
plot = Plot(min_border=0, border_fill_color="white", plot_width=1300, plot_height=700)
plot.title.text = "2009 Unemployment Data"
plot.toolbar_location = None
county_patches = Patches(xs="county_xs", ys="county_ys", fill_color=transform("rate", cmap), fill_alpha=0.7, line_color="white", line_width=0.5)
plot.add_glyph(county_source, county_patches)
state_patches = Patches(xs="state_xs", ys="state_ys", fill_alpha=0.0, line_color="#884444", line_width=2)
plot.add_glyph(state_source, state_patches)
cbar = ColorBar(color_mapper=cmap, location=(0, 0))
plot.add_layout(cbar, 'left')
doc = Document()
doc.add_root(plot)
if __name__ == "__main__":
doc.validate()
filename = "choropleth.html"
with open(filename, "w") as f:
def test_basic(object):
t = bt.transform("foo", "junk")
assert t == dict(field="foo", transform="junk")
def _get_scatter_plot_elements(
sp: Plot, source_pd: pd.DataFrame, x_col: str, y_col: str, label_cols: List[str],
colors: Dict[str, ColorMapper] = None, size: int = 4,
) -> Tuple[bokeh.plotting.Figure, Dict[str, List[LegendItem]], Legend, ColorBar, Dict[str, ColorMapper], List[Renderer]] :
if not source_pd.shape[0]:
print("WARN: No data to plot.")
return sp, None, None, None, None, None
sp.tools.append(HoverTool(tooltips=[(x_col, f'@{x_col}'), (y_col, f'@{y_col}')] +
[(c, f'@{c}') for c in source_pd.columns if c not in [x_col, y_col]]
))
cds = ColumnDataSource(source_pd)
if not label_cols:
sp.circle(x_col, y_col, source=cds, size=size)
return sp, None, None, None, None, None
continuous_cols = [col for col in label_cols if
(str(source_pd.dtypes[col]).startswith('float') or
str(source_pd.dtypes[col]).startswith('int'))]
factor_cols = [col for col in label_cols if col not in continuous_cols]
# Assign color mappers to columns
if colors is None:
colors = {}
color_mappers = {}
for col in continuous_cols:
low = np.nanmin(source_pd[col])
if np.isnan(low):
low = 0
high = 0
else:
high = np.nanmax(source_pd[col])
color_mappers[col] = colors[col] if col in colors else LinearColorMapper(palette='Magma256', low=low, high=high)
for col in factor_cols:
if col in colors:
color_mappers[col] = colors[col]
else:
factors = list(set(source_pd[col]))
color_mappers[col] = _get_categorical_palette(factors)
# Create initial glyphs
initial_col = label_cols[0]
initial_mapper = color_mappers[initial_col]
legend_items = {}
if not factor_cols:
all_renderers = [
sp.circle(x_col, y_col, color=transform(initial_col, initial_mapper), source=cds, size=size)
]
else:
all_renderers = []
legend_items = {col: DefaultDict(list) for col in factor_cols}
for key in source_pd.groupby(factor_cols).groups.keys():
key = key if len(factor_cols) > 1 else [key]
cds_view = CDSView(source=cds, filters=[GroupFilter(column_name=factor_cols[i], group=key[i]) for i in range(0, len(factor_cols))])
renderer = sp.circle(x_col, y_col, color=transform(initial_col, initial_mapper), source=cds, view=cds_view, size=size)
all_renderers.append(renderer)
for i in range(0, len(factor_cols)):
legend_items[factor_cols[i]][key[i]].append(renderer)
legend_items = {factor: [LegendItem(label=key, renderers=renderers) for key, renderers in key_renderers.items()] for factor, key_renderers in legend_items.items()}
# Add legend / color bar
legend = Legend(visible=False, click_policy='hide', orientation='vertical') if initial_col not in factor_cols else Legend(items=legend_items[initial_col], click_policy='hide', orientation='vertical')
color_bar = ColorBar(visible=False) if initial_col not in continuous_cols else ColorBar(color_mapper=color_mappers[initial_col])
sp.add_layout(legend, 'left')
sp.add_layout(color_bar, 'left')
return sp, legend_items, legend, color_bar, color_mappers, all_renderers
def test_transform():
t = bt.transform("foo", "junk")
assert t == dict(field="foo", transform="junk")
plot.yaxis.axis_label = 'Normalized Price'
aapl_source = ColumnDataSource(data=dict(
aapl_date=datetime(AAPL['date']),
aapl_close=AAPL['adj_close'],
))
goog_source = ColumnDataSource(data=dict(
goog_date=datetime(GOOG['date']),
goog_close=GOOG['adj_close'],
))
v_func = """
const first = xs[0]
const norm = new Float64Array(xs.length)
for (let i = 0; i < xs.length; i++) {
norm[i] = xs[i] / first
}
return norm
"""
normalize = CustomJSTransform(v_func=v_func)
plot.line(x='aapl_date', y=transform('aapl_close', normalize), line_width=2,
color='#cf3c4d', alpha=0.6,legend="Apple", source=aapl_source)
plot.line(x='goog_date', y=transform('goog_close', normalize), line_width=2,
color='#2f7bce', alpha=0.6, legend="Google", source=goog_source)
plot.legend.location='top_left'
output_file("customjs_transform.html")
show(plot)
gender_transform = CustomJSTransform(args=dict(source=ages), func="", v_func="""
var val = new Float64Array(xs.length)
for (var i = 0; i < xs.length; i++) {
if (source.data['Sex'][i] == 'Male')
val[i] = -xs[i]
else
val[i] = xs[i]
}
return val
""")
pyramid = figure(plot_width=600, plot_height=500, toolbar_location=None, y_range=groups,
title="Population Breakdown by Age Group and Gender",
x_axis_label="Population (Millions)",y_axis_label="Age Group")
pyramid.hbar(y="AgeGrp", height=1, right=transform('Value', gender_transform),
source=ages, legend="Sex", line_color="white",
fill_color=factor_cmap('Sex', palette=["#3B8686", "#CFF09E"], factors=["Male", "Female"]))
pyramid.ygrid.grid_line_color = None
pyramid.xaxis[0].formatter = FuncTickFormatter(code="""
return (Math.abs(tick) / 1e6) + " M"
""")
# line plot of known and predicted population
known = ColumnDataSource(data=dict(x=[], y=[]))
predicted = ColumnDataSource(data=dict(x=[], y=[]))
population = figure(plot_width=600, plot_height=180, toolbar_location=None,
title="Total Population by Year",
