def save_plot_to_file(traces, num_traces, outfile):
"""Save plot figure to file."""
colors = itertools.cycle(palette)
xrange = range(len(traces[0]))
plot = figure(plot_width=800)
plot.add_tools(tools.CrosshairTool())
plot.add_tools(tools.HoverTool())
for i in range(min(len(traces), num_traces)):
plot.line(xrange, traces[i], line_color=next(colors))
output_file(outfile)
show(plot)
def make_plot(amount):
# call function with desired amount
mortgage = calculate_mortgage(float(amount))
# convert the dataframe returned by calculate_mortgage() into a ColumnDataSource (to be used by Bokeh)
mortgage_cds = convert_df_to_cds(mortgage)
stacks = ['pay', 'capital', 'interest']
colors_arr = ["#c9d9d3", "#718dbf", "#e84d60"]
p = figure(title="Mortgage repayment over time",
plot_width=600,
plot_height=600,
x_axis_label='x',
y_axis_label='y')
p.vbar_stack(stacks,
source=mortgage_cds,
x='year',
width=0.9,
fill_alpha=0.5,
color=colors_arr,
line_color='black')
# refer to data with @ and
# to graph properties, e.g. x and y, with $
h = tools.HoverTool(tooltips=[(
'Year: ',
'@year'), ('Capital left to repay',
'@pay'), ('Repayment on interests',
'@interest'), ('Repayment on capital',
'@capital')])
# add tool to the graph
p.add_tools(h)
output_notebook()
return p
# reg_plot.line(x=runs.freq, y=runs.power, source=source_2,
# line_width=line_width,
# color=colors[2],
# legend='Cannibalism: {}'.format(np.round(param.cannib_2, 3)))
# reg_plot.line(x=runs.freq, y=runs.power, source=source_3,
# line_width=line_width,
# color=colors[3],
# legend='Cannibalism: {}'.format(np.round(param.cannib_3, 3)))
reg_plot.line(x=runs.freq, y=runs.power, source=source_4,
line_width=line_width,
color=colors[4],
legend='Cannibalism: {}'.format(np.round(param.cannib_4, 3)))
reg_hover = tools.HoverTool()
reg_hover.tooltips = [
('Frequency', '@freq'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'),
('Source', '@comb')
]
reg_plot.add_tools(reg_hover)
reg_plot.legend.location = "bottom_right"
reg_plot.legend.label_text_font_size = legend_font_size
reg_plot.title.text_font_size = title_font_size
reg_plot.yaxis.axis_line_width = axis_line_width
reg_plot.xaxis.axis_line_width = axis_line_width
def periodogram_plotter(self, dataframes: dict,
title: str):
"""
Create the bokeh plots for periodograms, mean and median
Args:
dataframes: the source data
title: title of data
Returns:
Array of bokeh plots
"""
data_sources = self.periodogram_source(dataframes)
plot_labels = [mean, median]
table_plots = {}
for table_name in tables:
table_title = table_name.split('_')[1]
column_plots = {}
for column_name in columns:
column_title = column_name.split('_')[1]
regular_plot = plt.figure()
regular_plot.title.text = '{} Periodogram for {} genotype {}'.\
format(title, table_title, column_title)
regular_plot.yaxis.axis_label = 'Power Spectral Density'
regular_plot.xaxis.axis_label = 'Frequency'
log_plot = plt.figure(y_axis_type='log')
log_plot.title.text = '{} Log-Scale Periodogram for {} ' \
'genotype {}'. \
format(title, table_title, column_title)
log_plot.yaxis.axis_label = 'log(Power Spectral Density)'
log_plot.xaxis.axis_label = 'Frequency'
for index, label_name in enumerate(plot_labels):
source = data_sources[label_name][table_name][column_name]
regular_plot.line(x=freq, y=power, source=source,
color=colors[index],
legend=label_name)
log_plot.line(x=freq, y=power, source=source,
color=colors[index],
legend=label_name)
regular_hover = tools.HoverTool()
regular_hover.tooltips = [
('Frequency', '@freq'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'),
('Source', '@comb')
]
regular_plot.add_tools(regular_hover)
log_hover = tools.HoverTool()
log_hover.tooltips = [
('Frequency', '@freq'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'),
('Source', '@comb')
]
log_plot.add_tools(log_hover)
column_plots[column_name] = [regular_plot, log_plot]
table_plots[table_name] = column_plots
return table_plots
this_plot.circle(
source=source_female,
x="total_bill",
y="tip",
color="darkorange",
size=10,
alpha=0.7,
legend="Women",
)
# Set axis labels
this_plot.xaxis.axis_label = "Total Bill"
this_plot.yaxis.axis_label = "Tip Amount"
# Show information when hovering the mouse over datapoints
this_plot.add_tools(tools.HoverTool(tooltips=[("Day",
"@day")])) # @ chooses feature
# Hide all circles of a given category when clicked in legend
this_plot.legend.click_policy = "hide"
output_notebook()
show(this_plot)
# %% [markdown] {"slideshow": {"slide_type": "slide"}}
# # Pivot table plots
# %%
from pivottablejs import pivot_ui
pivot_ui(tips)
# %% [markdown] {"slideshow": {"slide_type": "slide"}}
def periodogram_plotter(periodogram_mean_source, periodogram_median_source,
life_stage_title: str):
"""
Create a set of periodograms
Args:
periodogram_mean_source: mean data periodogram
periodogram_median_source: median data periodogram
life_stage_title: name for life stage
Returns:
a plot system to show
"""
mean_plot = plt.figure()
mean_plot.title.text = '{} Mean Periodogram'.format(life_stage_title)
mean_plot.yaxis.axis_label = 'Power Spectral Density'
mean_plot.xaxis.axis_label = 'Frequency'
mean_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_resistant'],
color=colors[0], legend='Resistant')
mean_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_heterozygous'],
color=colors[1], legend='Heterozygous')
mean_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_susceptible'],
color=colors[2], legend='Susceptible')
mean_hover = tools.HoverTool()
mean_hover.tooltips = [
('Frequency', '@frequency'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype')
]
mean_plot.add_tools(mean_hover)
median_plot = plt.figure()
median_plot.title.text = '{} Median Periodogram'.format(life_stage_title)
median_plot.yaxis.axis_label = 'Power Spectral Density'
median_plot.xaxis.axis_label = 'Frequency'
median_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_resistant'],
color=colors[0], legend='Resistant')
median_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_heterozygous'],
color=colors[1], legend='Heterozygous')
median_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_susceptible'],
color=colors[2], legend='Susceptible')
median_hover = tools.HoverTool()
median_hover.tooltips = [
('Frequency', '@frequency'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype')
]
median_plot.add_tools(median_hover)
mean_log_plot = plt.figure(y_axis_type='log')
mean_log_plot.title.text = '{} Mean Log-Scale Periodogram'.\
format(life_stage_title)
mean_log_plot.yaxis.axis_label = 'log(Power Spectral Density)'
mean_log_plot.xaxis.axis_label = 'Frequency'
mean_log_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_resistant'],
color=colors[0], legend='Resistant')
mean_log_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_heterozygous'],
color=colors[1], legend='Heterozygous')
mean_log_plot.line(x='frequency', y='power',
source=periodogram_mean_source['genotype_susceptible'],
color=colors[2], legend='Susceptible')
mean_log_hover = tools.HoverTool()
mean_log_hover.tooltips = [
('Frequency', '@frequency'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype')
]
mean_log_plot.add_tools(mean_log_hover)
median_log_plot = plt.figure(y_axis_type='log')
median_log_plot.title.text = '{} Median Log-Scale Periodogram'. \
format(life_stage_title)
median_log_plot.yaxis.axis_label = 'log(Power Spectral Density)'
median_log_plot.xaxis.axis_label = 'Frequency'
median_log_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_resistant'],
color=colors[0], legend='Resistant')
median_log_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_heterozygous'],
color=colors[1], legend='Heterozygous')
median_log_plot.line(x='frequency', y='power',
source=periodogram_median_source['genotype_susceptible'],
color=colors[2], legend='Susceptible')
median_log_hover = tools.HoverTool()
median_log_hover.tooltips = [
('Frequency', '@frequency'),
('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype')
]
median_log_plot.add_tools(median_log_hover)
return lay.gridplot([[mean_plot, median_plot],
[mean_log_plot, median_log_plot]],
toolbar_location='left')
def create_figure(df_exploded, df_plots, wdg, cols, explode_val=None, explode_group=None):
'''
Create and return a figure based on the data in a dataframe and widget configuration.
Args:
df_exploded (pandas dataframe): Dataframe of just the data that will be plotted in this figure.
df_plots (pandas dataframe): Dataframe of all plots data, used only for maintaining consistent series colors.
wdg (ordered dict): Dictionary of bokeh model widgets.
cols (dict): Keys are categories of columns of df_source, and values are a list of columns of that category.
explode_val (string, optional): The value in the column designated by wdg['explode'] that applies to this figure.
explode_group (string, optional): The value in the wdg['explode_group'] column that applies to this figure.
Returns:
p (bokeh.model.figure): A figure, with all glyphs added by the add_glyph() function.
'''
# If x_group has a value, create a combined column in the dataframe for x and x_group
x_col = wdg['x'].value
if wdg['x_group'].value != 'None':
x_col = str(wdg['x_group'].value) + '_' + str(wdg['x'].value)
df_exploded[x_col] = df_exploded[wdg['x_group'].value].map(str) + ' ' + df_exploded[wdg['x'].value].map(str)
#Build x and y ranges and figure title
kw = dict()
#Set x and y ranges. When x is grouped, there is added complication of separating the groups
xs = df_exploded[x_col].values.tolist()
ys = df_exploded[wdg['y'].value].values.tolist()
if wdg['x_group'].value != 'None':
kw['x_range'] = []
unique_groups = df_exploded[wdg['x_group'].value].unique().tolist()
unique_xs = df_exploded[wdg['x'].value].unique().tolist()
for i, ugr in enumerate(unique_groups):
for uxs in unique_xs:
kw['x_range'].append(str(ugr) + ' ' + str(uxs))
#Between groups, add entries that consist of spaces. Increase number of spaces from
#one break to the next so that each entry is unique
kw['x_range'].append(' ' * (i + 1))
elif wdg['x'].value in cols['discrete']:
kw['x_range'] = sorted(set(xs))
if wdg['y'].value in cols['discrete']:
kw['y_range'] = sorted(set(ys))
#Set figure title
kw['title'] = wdg['plot_title'].value
seperator = '' if kw['title'] == '' else ', '
if explode_val is not None:
if explode_group is not None:
kw['title'] = kw['title'] + seperator + "%s = %s" % (wdg['explode_group'].value, str(explode_group))
seperator = '' if kw['title'] == '' else ', '
kw['title'] = kw['title'] + seperator + "%s = %s" % (wdg['explode'].value, str(explode_val))
#Add figure tools
hover = bmt.HoverTool(
tooltips=[
("ser", "@ser_legend"),
("x", "@x_legend"),
("y", "@y_legend"),
]
)
TOOLS = [bmt.BoxZoomTool(), bmt.PanTool(), hover, bmt.ResetTool(), bmt.SaveTool()]
#Create figure with the ranges, titles, and tools, and adjust formatting and labels
p = bp.figure(plot_height=int(wdg['plot_height'].value), plot_width=int(wdg['plot_width'].value), tools=TOOLS, **kw)
p.toolbar.active_drag = TOOLS[0]
p.title.text_font_size = wdg['plot_title_size'].value + 'pt'
p.xaxis.axis_label = wdg['x_title'].value
p.yaxis.axis_label = wdg['y_title'].value
p.xaxis.axis_label_text_font_size = wdg['x_title_size'].value + 'pt'
p.yaxis.axis_label_text_font_size = wdg['y_title_size'].value + 'pt'
p.xaxis.major_label_text_font_size = wdg['x_major_label_size'].value + 'pt'
p.yaxis.major_label_text_font_size = wdg['y_major_label_size'].value + 'pt'
p.xaxis.major_label_orientation = 'horizontal' if wdg['x_major_label_orientation'].value == '0' else math.radians(float(wdg['x_major_label_orientation'].value))
if wdg['x'].value in cols['continuous']:
if wdg['x_min'].value != '': p.x_range.start = float(wdg['x_min'].value)
if wdg['x_max'].value != '': p.x_range.end = float(wdg['x_max'].value)
if wdg['y'].value in cols['continuous']:
if wdg['y_min'].value != '': p.y_range.start = float(wdg['y_min'].value)
if wdg['y_max'].value != '': p.y_range.end = float(wdg['y_max'].value)
#Add glyphs to figure
c = C_NORM
if wdg['series'].value == 'None':
if wdg['y_agg'].value != 'None' and wdg['y'].value in cols['continuous']:
xs = df_exploded[x_col].values.tolist()
ys = df_exploded[wdg['y'].value].values.tolist()
add_glyph(wdg, p, xs, ys, c)
else:
full_series = df_plots[wdg['series'].value].unique().tolist() #for colors only
if wdg['chart_type'].value in STACKEDTYPES: #We are stacking the series
xs_full = sorted(df_exploded[x_col].unique().tolist())
y_bases_pos = [0]*len(xs_full)
y_bases_neg = [0]*len(xs_full)
for i, ser in enumerate(df_exploded[wdg['series'].value].unique().tolist()):
c = COLORS[full_series.index(ser)]
df_series = df_exploded[df_exploded[wdg['series'].value].isin([ser])]
xs_ser = df_series[x_col].values.tolist()
ys_ser = df_series[wdg['y'].value].values.tolist()
if wdg['chart_type'].value not in STACKEDTYPES: #The series will not be stacked
add_glyph(wdg, p, xs_ser, ys_ser, c, series=ser)
else: #We are stacking the series
ys_pos = [ys_ser[xs_ser.index(x)] if x in xs_ser and ys_ser[xs_ser.index(x)] > 0 else 0 for i, x in enumerate(xs_full)]
ys_neg = [ys_ser[xs_ser.index(x)] if x in xs_ser and ys_ser[xs_ser.index(x)] < 0 else 0 for i, x in enumerate(xs_full)]
ys_stacked_pos = [ys_pos[i] + y_bases_pos[i] for i in range(len(xs_full))]
ys_stacked_neg = [ys_neg[i] + y_bases_neg[i] for i in range(len(xs_full))]
add_glyph(wdg, p, xs_full, ys_stacked_pos, c, y_bases=y_bases_pos, series=ser)
add_glyph(wdg, p, xs_full, ys_stacked_neg, c, y_bases=y_bases_neg, series=ser)
y_bases_pos = ys_stacked_pos
y_bases_neg = ys_stacked_neg
return p
def __init__(self,
source: Source,
train_data_source: Optional[ColumnDataSource] = None,
num_samples: int = 0,
plot_marker: bool = False,
xlabel: str = 'x',
ylabel: str = 'y',
**kargs: Any):
# Number of samples currently added to the plot
self._num_samples: int = 0
self._sample_renderers: List[GlyphRenderer] = []
if isinstance(source, dict):
source = ColumnDataSource(data=source)
x = source.data["x"]
mu = source.data["mu"]
cov_diag = np.diag(source.data["cov"])
uncertainty = 1.96 * np.sqrt(cov_diag)
assert (len(mu.shape) == 1)
source.data["lower"] = mu - uncertainty
source.data["upper"] = mu + uncertainty
source.data["var"] = cov_diag
# Get the appropriated minumum and maximum for the plot y range
min_y, max_y = np.min(mu - uncertainty), np.max(mu + uncertainty)
min_x, max_x = 1.02 * np.min(x), 1.02 * np.max(x)
min_y, max_y = 1.05 * min_y, 1.05 * max_y
# Note that we will add HoverTool later
if "width" not in kargs:
kargs["width"] = 900
if "height" not in kargs:
kargs["height"] = 400
if "y_range" in kargs:
fig = figure(x_range=(min_x, max_x), **kargs)
else:
fig = figure(x_range=(min_x, max_x),
y_range=(min_y, max_y),
**kargs)
fig.xaxis.axis_label = xlabel
fig.yaxis.axis_label = ylabel
prediction_plot = fig.line("x",
"mu",
source=source,
line_width=2,
legend_label="Prediction Mean")
if plot_marker:
prediction_plot = fig.circle("x",
"mu",
source=source,
legend_label="Prediction Mean")
hover1 = tools.HoverTool()
hover1.renderers = [prediction_plot]
hover1.tooltips = [("x", "@x"), ("Mean", "@mu"),
("Mean + 2σ", "@upper"), ("Mean - 2σ", "@lower"),
("Var", "@var")]
fig.add_tools(hover1)
band = Band(base="x",
lower="lower",
upper="upper",
source=source,
level='image',
fill_color="#e0ffff",
fill_alpha=0.8)
# Plot the training data
if train_data_source is not None:
cross_plot = fig.cross("x",
"y",
source=train_data_source,
size=10,
color="red",
legend_label="Train")
hover2 = tools.HoverTool()
hover2.tooltips = [("Training Point", "(@x, @y)")]
hover2.renderers = [cross_plot]
fig.add_tools(hover2)
fig.add_layout(band)
fig.legend.click_policy = "hide"
self._source: ColumnDataSource = source
self._fig: Figure = fig
if num_samples > 0:
self.add_samples(num_samples)
def plot_gp(source: Source,
train_data_source: Optional[ColumnDataSource] = None,
samples: Optional[np.ndarray] = None,
plot_marker: bool = False,
xlabel: str = 'x',
ylabel: str = 'y',
dont_show: bool = False,
**kargs: Any) -> Optional[Figure]:
"""
Plot a Gaussian Process.
Parameters
----------
source : Source
Either a bokeh ColumnDataSource of a dictionary containing at least the
fields 'x', 'mu' and 'cov', where 'x' is a range of values,
'mu' is the predicted average function response for the range of values
in 'x', and `cov` is covariance matrix.
train_data_source : ColumnDataSource, None
Optional ColumnDataSource containing a 'x' and 'y' columns with
training data
samples : np.ndarray
A 2D numpy array or an integer. In the first two cases each element is
ploted by the 'x' values in `source`. If an int is passed, then a
multivariate Gaussian distribution is generated using `mu` and `cov` in
`source`. A maximum of four samples is possible.
plot_marker : bool
If predicted points should be marked with a circle or not.
xlabel : str
Label of the 'x' axis (default is "x").
ylabel : str
Label of the 'y' axis (default is "y").
dont_show : bool
If the plot should not be show and the figure should be returned
instead. Default is False.
kargs : dict
The remaining arguments captured in `kargs` are passed to bokeh figure.
Ex: width, height, title, etc.
Returns
-------
figure or None
Returns the bokeh figure if `dont_show` is True.
"""
if isinstance(source, dict):
source = ColumnDataSource(data=source)
x: np.ndarray = source.data["x"]
mu: np.ndarray = source.data["mu"]
cov_diag: np.ndarray = np.diag(source.data["cov"])
uncertainty: np.ndarray = 1.96 * np.sqrt(cov_diag)
assert (len(mu.shape) == 1)
source.data["lower"] = mu - uncertainty
source.data["upper"] = mu + uncertainty
source.data["var"] = cov_diag
# Get the appropriated minumum and maximum for the plot y range
min_y, max_y = np.min(mu - uncertainty), np.max(mu + uncertainty)
min_x, max_x = 1.02 * np.min(x), 1.02 * np.max(x)
if samples is not None:
if isinstance(samples, int):
cov = source.data["cov"]
samples = np.random.multivariate_normal(mu, cov, samples)
min_y, max_y = min(min_y, np.min(samples)), max(max_y, np.max(samples))
min_y, max_y = 1.05 * min_y, 1.05 * max_y
# Note that we will add HoverTool later
if "width" not in kargs:
kargs["width"] = 900
if "height" not in kargs:
kargs["height"] = 400
if "y_range" in kargs:
p = figure(x_range=(min_x, max_x), **kargs)
else:
p = figure(x_range=(min_x, max_x), y_range=(min_y, max_y), **kargs)
p.xaxis.axis_label = xlabel
p.yaxis.axis_label = ylabel
prediction_plot = p.line("x",
"mu",
source=source,
line_width=2,
legend_label="Prediction Mean")
if plot_marker:
prediction_plot = p.circle("x",
"mu",
source=source,
legend_label="Prediction Mean")
hover1 = tools.HoverTool()
hover1.renderers = [prediction_plot]
hover1.tooltips = [("x", "@x"), ("Mean", "@mu"), ("Mean + 2σ", "@upper"),
("Mean - 2σ", "@lower"), ("Var", "@var")]
p.add_tools(hover1)
band = Band(base="x",
lower="lower",
upper="upper",
source=source,
level='image',
fill_color="#e0ffff",
fill_alpha=0.8)
if samples is not None:
for i, sample in enumerate(samples):
p.line(x,
sample,
color=palette[i],
legend_label=f"Sample {i}",
line_dash="dashed")
# Plot the training data
if train_data_source is not None:
cross_plot = p.cross("x",
"y",
source=train_data_source,
size=10,
color="red",
legend_label="Train")
hover2 = tools.HoverTool()
hover2.tooltips = [("Training Point", "(@x, @y)")]
hover2.renderers = [cross_plot]
p.add_tools(hover2)
p.add_layout(band)
p.legend.click_policy = "hide"
if dont_show:
return p
show(p)
return None
def _plot_periodogram(dataframe_low: hint.dataframe,
dataframe_high: hint.dataframe, title: str) -> dict:
"""
Create a Bokeh plot of the periodogram dataframe
Args:
dataframe_low: the dataframe low survival
dataframe_high: the dataframe high survival
title: the title for the plot
Returns:
a dictionary of Bokeh plots
"""
source_low = mdl.ColumnDataSource(dataframe_low)
source_high = mdl.ColumnDataSource(dataframe_high)
base_title = 'Main period: Low: {} or High: {}'. \
format(np.round(dataframe_low[runs.primary].iloc[0], 3),
np.round(dataframe_high[runs.primary].iloc[0], 3))
reg_plot = plt.figure(plot_height=plot_height, plot_width=plot_width)
reg_plot.title.text = base_title
reg_plot.xaxis.axis_label = 'Frequency'
reg_plot.yaxis.axis_label = 'Power Spectral Density'
reg_plot.line(x=runs.freq,
y=runs.power,
source=source_low,
line_width=line_width,
color=colors[0],
legend='Survival: {}'.format(
np.round(param.larva_prob_bt_low_ss, 3)))
reg_plot.line(x=runs.freq,
y=runs.power,
source=source_high,
line_width=line_width,
color=colors[1],
legend='Survival: {}'.format(
np.round(param.larva_prob_bt_high_ss, 3)))
reg_hover = tools.HoverTool()
reg_hover.tooltips = [('Frequency', '@freq'), ('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'), ('Source', '@comb')]
reg_plot.add_tools(reg_hover)
reg_plot.legend.location = "top_right"
reg_plot.legend.label_text_font_size = legend_font_size
reg_plot.title.text_font_size = title_font_size
reg_plot.yaxis.axis_line_width = axis_line_width
reg_plot.xaxis.axis_line_width = axis_line_width
reg_plot.yaxis.axis_label_text_font_size = axis_font_size
reg_plot.xaxis.axis_label_text_font_size = axis_font_size
reg_plot.yaxis.major_label_text_font_size = axis_tick_font_size
reg_plot.xaxis.major_label_text_font_size = axis_tick_font_size
reg_plot.ygrid.grid_line_width = grid_line_width
reg_plot.xgrid.grid_line_width = grid_line_width
log_plot = plt.figure(plot_height=plot_height,
plot_width=plot_width,
y_axis_type='log')
log_plot.title.text = 'Log-scale {}'. \
format(base_title)
log_plot.xaxis.axis_label = 'Frequency'
log_plot.yaxis.axis_label = 'log(Power Spectral Density)'
log_plot.line(x=runs.freq,
y=runs.power,
source=source_low,
line_width=line_width,
color=colors[0],
legend='Survival: {}'.format(
np.round(param.larva_prob_bt_low_ss, 3)))
log_plot.line(x=runs.freq,
y=runs.power,
source=source_high,
line_width=line_width,
color=colors[1],
legend='Survival: {}'.format(
np.round(param.larva_prob_bt_high_ss, 3)))
log_hover = tools.HoverTool()
log_hover.tooltips = [('Frequency', '@freq'), ('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'), ('Source', '@comb')]
log_plot.add_tools(log_hover)
log_plot.legend.location = "top_right"
log_plot.legend.label_text_font_size = legend_font_size
log_plot.title.text_font_size = title_font_size
log_plot.yaxis.axis_line_width = axis_line_width
log_plot.xaxis.axis_line_width = axis_line_width
log_plot.yaxis.axis_label_text_font_size = axis_font_size
log_plot.xaxis.axis_label_text_font_size = axis_font_size
log_plot.yaxis.major_label_text_font_size = axis_tick_font_size
log_plot.xaxis.major_label_text_font_size = axis_tick_font_size
log_plot.ygrid.grid_line_width = grid_line_width
log_plot.xgrid.grid_line_width = grid_line_width
return {runs.reg: reg_plot, runs.log: log_plot}
def _plot_periodogram(dataframe: hint.dataframe, title: str) -> dict:
"""
Create a Bokeh plot of the periodogram dataframe
Args:
dataframe: the dataframe to use
title: the title for the plot
Returns:
a dictionary of Bokeh plots
"""
source = mdl.ColumnDataSource(dataframe)
base_title = 'Main period: {}'.\
format(np.round(dataframe[runs.primary].iloc[0], 3))
reg_plot = plt.figure(plot_height=plot_height, plot_width=plot_width)
reg_plot.title.text = base_title
reg_plot.xaxis.axis_label = 'Frequency'
reg_plot.yaxis.axis_label = 'Power Spectral Density'
reg_plot.line(x=runs.freq,
y=runs.power,
source=source,
line_width=line_width,
color=colors[0])
reg_hover = tools.HoverTool()
reg_hover.tooltips = [('Frequency', '@freq'), ('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'), ('Source', '@comb')]
reg_plot.add_tools(reg_hover)
reg_plot.title.text_font_size = title_font_size
reg_plot.yaxis.axis_line_width = axis_line_width
reg_plot.xaxis.axis_line_width = axis_line_width
reg_plot.yaxis.axis_label_text_font_size = axis_font_size
reg_plot.xaxis.axis_label_text_font_size = axis_font_size
reg_plot.yaxis.major_label_text_font_size = axis_tick_font_size
reg_plot.xaxis.major_label_text_font_size = axis_tick_font_size
reg_plot.ygrid.grid_line_width = grid_line_width
reg_plot.xgrid.grid_line_width = grid_line_width
log_plot = plt.figure(plot_height=plot_height,
plot_width=plot_width,
y_axis_type='log')
log_plot.title.text = 'Log-scale {}'.\
format(base_title)
log_plot.xaxis.axis_label = 'Frequency'
log_plot.yaxis.axis_label = 'log(Power Spectral Density)'
log_plot.line(x=runs.freq,
y=runs.power,
source=source,
line_width=line_width,
color=colors[0])
log_hover = tools.HoverTool()
log_hover.tooltips = [('Frequency', '@freq'), ('Period', '@period'),
('Spectral Density', '@power'),
('Genotype', '@genotype'), ('Source', '@comb')]
log_plot.add_tools(log_hover)
log_plot.title.text_font_size = title_font_size
log_plot.yaxis.axis_line_width = axis_line_width
log_plot.xaxis.axis_line_width = axis_line_width
log_plot.yaxis.axis_label_text_font_size = axis_font_size
log_plot.xaxis.axis_label_text_font_size = axis_font_size
log_plot.yaxis.major_label_text_font_size = axis_tick_font_size
log_plot.xaxis.major_label_text_font_size = axis_tick_font_size
log_plot.ygrid.grid_line_width = grid_line_width
log_plot.xgrid.grid_line_width = grid_line_width
return {runs.reg: reg_plot, runs.log: log_plot}
def add_tools(self,
chart: Chart,
df: DataFrame,
center_name: str,
absolute: bool,
ordinal: bool,
use_adjusted_intervals: bool):
self.add_ci_to_chart_datasources(chart,
df,
center_name,
ordinal,
use_adjusted_intervals)
LOWER, UPPER = ((ADJUSTED_LOWER, ADJUSTED_UPPER)
if use_adjusted_intervals
else (CI_LOWER, CI_UPPER))
if len(chart.figure.legend) > 0:
chart.figure.legend.click_policy = "hide"
axis_format, y_min, y_max = axis_format_precision(
numbers=(df[LOWER]
.append(df[center_name])
.append(df[UPPER])
.append(df[NULL_HYPOTHESIS]
if NULL_HYPOTHESIS in df.columns
else None)
),
absolute=absolute,
extra_zeros=2)
ordinal_tool_tip = (
[] if not ordinal else
[(self._ordinal_group_column, f"@{self._ordinal_group_column}")]
)
p_value_tool_tip = (
([("p-value", "@p_value{0.0000}")] +
([("adjusted p-value", "@adjusted_p{0.0000}")]
if len(df) > 1 else []))
if center_name == DIFFERENCE else [])
nim_tool_tip = (
[("null hypothesis", f"@null_hyp{{{axis_format}}}")]
if NULL_HYPOTHESIS in df.columns else [])
tooltips = (
[("group", "@color")] +
ordinal_tool_tip +
[(f"{center_name}", f"@{center_name}{{{axis_format}}}")] +
[(("adjusted " if use_adjusted_intervals else "") +
"confidence interval",
f"(@{{{LOWER}}}{{{axis_format}}},"
f" @{{{UPPER}}}{{{axis_format}}})")] +
p_value_tool_tip +
nim_tool_tip
)
lines_with_hover = [] if ordinal else ['center', 'nim']
hover = tools.HoverTool(tooltips=tooltips, names=lines_with_hover)
box_zoom = tools.BoxZoomTool()
chart.figure.add_tools(hover,
tools.ZoomInTool(),
tools.ZoomOutTool(),
box_zoom,
tools.PanTool(),
tools.ResetTool())
chart.figure.toolbar.active_drag = box_zoom
