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Option to use plotly templates
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@alubbock
alubbock committed Feb 13, 2020
1 parent d34d09f commit fa7262c
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Showing 2 changed files with 50 additions and 14 deletions.
1 change: 1 addition & 0 deletions thunor/config.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
plotly_template = 'none' # https://plot.ly/python/templates/
63 changes: 49 additions & 14 deletions thunor/plots.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
# -*- coding: utf-8 -*-

import plotly.graph_objs as go
import numpy as np
import seaborn as sns
import thunor.config as config
from .helpers import format_dose
from .dip import ctrl_dip_rates, expt_dip_rates
from thunor.curve_fit import HillCurveNull, is_param_truncated
Expand Down Expand Up @@ -170,7 +173,7 @@ def _combine_title_subtitle(title, subtitle):


def plot_drc(fit_params, is_absolute=False, color_by=None, color_groups=None,
title=None, subtitle=None):
title=None, subtitle=None, template=config.plotly_template):
"""
Plot dose response curve fits
Expand All @@ -191,6 +194,8 @@ def plot_drc(fit_params, is_absolute=False, color_by=None, color_groups=None,
Title (or None to auto-generate)
subtitle: str, optional
Subtitle (or None to auto-generate)
template: str
Name of plotly template (https://plot.ly/python/templates/)
Returns
-------
Expand Down Expand Up @@ -411,11 +416,12 @@ def plot_drc(fit_params, is_absolute=False, color_by=None, color_groups=None,
name=repl_name)
)
if ctrl_resp is not None:
ctrl_color = 'white' if template == 'plotly_dark' else 'black'
traces.append(go.Scatter(x=ctrl_doses,
y=ctrl_resp,
mode='markers',
marker={'symbol': shape,
'color': 'black',
'color': ctrl_color,
'size': 5},
hoverinfo='y+text',
text=ctrl_name,
Expand Down Expand Up @@ -479,13 +485,15 @@ def plot_drc(fit_params, is_absolute=False, color_by=None, color_groups=None,
'rangemode': yaxis_rangemode
},
annotations=annotations,
template=template
)

return go.Figure(data=traces, layout=layout)


def plot_drug_combination_heatmap(ctrl_resp_data, expt_resp_data,
title=None, subtitle=None):
def plot_drug_combination_heatmap(
ctrl_resp_data, expt_resp_data, title=None, subtitle=None,
template=config.plotly_template):
"""
Plot heatmap of drug combination response by DIP rate
Expand All @@ -502,6 +510,8 @@ def plot_drug_combination_heatmap(ctrl_resp_data, expt_resp_data,
Title (or None to auto-generate)
subtitle: str, optional
Subtitle (or None to auto-generate)
template: str
Name of plotly template (https://plot.ly/python/templates/)
Returns
-------
Expand Down Expand Up @@ -574,7 +584,8 @@ def plot_drug_combination_heatmap(ctrl_resp_data, expt_resp_data,
},
yaxis={
'title': '{} concentration'.format(drug1)
}
},
template=template
)

return go.Figure(data=[trace], layout=layout)
Expand Down Expand Up @@ -606,7 +617,8 @@ def _symbols_hovertext_two_dataset_scatter(df_params, range_bounded_params,


def plot_two_dataset_param_scatter(df_params, fit_param, title, subtitle,
color_by, color_groups, **kwargs):
color_by, color_groups,
template=config.plotly_template, **kwargs):
"""
Plot a parameter comparison across two datasets
Expand All @@ -620,6 +632,8 @@ def plot_two_dataset_param_scatter(df_params, fit_param, title, subtitle,
Title (or None to auto-generate)
subtitle: str, optional
Subtitle (or None to auto-generate)
template: str
Name of plotly template (https://plot.ly/python/templates/)
kwargs: dict, optional
Additional keyword arguments
Expand Down Expand Up @@ -801,6 +815,7 @@ def plot_two_dataset_param_scatter(df_params, fit_param, title, subtitle,
'type': 'log' if _param_is_log(fit_param) else None}
layout['hovermode'] = 'closest'
layout['showlegend'] = color_by is not None
layout['template'] = template

return go.Figure(layout=layout, data=data)

Expand Down Expand Up @@ -830,6 +845,7 @@ def plot_drc_params(df_params, fit_param,
multi_dataset=False,
color_by=None,
color_groups=None,
template=config.plotly_template,
**kwargs):
"""
Box, bar, or scatter plots of DIP rate fit parameters
Expand Down Expand Up @@ -862,6 +878,8 @@ def plot_drc_params(df_params, fit_param,
(default)
color_groups: dict or None
Groups of cell lines of drugs to color by
template: str
Name of plotly template (https://plot.ly/python/templates/)
kwargs: dict, optional
Additional keyword arguments
Expand Down Expand Up @@ -924,6 +942,7 @@ def plot_drc_params(df_params, fit_param,
yaxis_title)

layout = dict(title=title,
template=template,
yaxis={'title': yaxis_title,
'type': 'log' if _param_is_log(fit_param) else None})

Expand Down Expand Up @@ -1404,7 +1423,8 @@ def _create_label_max_items(items, max_items=5):

def plot_time_course(hts_pandas,
log_yaxis=False, assay_name='Assay', title=None,
subtitle=None, show_dip_fit=False):
subtitle=None, show_dip_fit=False,
template=config.plotly_template):
"""
Plot a dose response time course
Expand All @@ -1423,6 +1443,8 @@ def plot_time_course(hts_pandas,
Subtitle (or None to auto-generate)
show_dip_fit: bool
Overlay the DIP rate fit on the time course
template: str
Name of plotly template (https://plot.ly/python/templates/)
Returns
-------
Expand Down Expand Up @@ -1478,6 +1500,8 @@ def plot_time_course(hts_pandas,
colours = _sns_to_rgb(sns.color_palette(
"husl", len(df_doses.index.get_level_values(level='dose').unique())))

ctrl_color = 'white' if template == 'plotly_dark' else 'black'

if show_dip_fit:
if df_controls is not None:
dip_rate_ctrl = ctrl_dip_rates(df_controls)
Expand All @@ -1502,7 +1526,7 @@ def plot_time_course(hts_pandas,
x=x_range,
y=timecourse,
mode='lines+markers',
line={'color': 'black',
line={'color': ctrl_color,
'shape': 'spline',
'dash': 'dot' if show_dip_fit else None},
marker={'size': 5},
Expand All @@ -1525,7 +1549,7 @@ def plot_time_course(hts_pandas,
x=minmax,
y=dip_points,
mode='lines',
line={'color': 'black'},
line={'color': ctrl_color},
marker={'size': 5},
name='DIP fit Control',
legendgroup='__Control',
Expand Down Expand Up @@ -1593,11 +1617,13 @@ def plot_time_course(hts_pandas,
'dtick': 12},
yaxis={'title': assay_name,
'range': (-2, 7) if log_yaxis else None},
template=template
)
return go.Figure(data=data, layout=layout)


def plot_ctrl_dip_by_plate(df_controls, title=None, subtitle=None):
def plot_ctrl_dip_by_plate(df_controls, title=None, subtitle=None,
template=config.plotly_template):
"""
Parameters
Expand All @@ -1608,6 +1634,8 @@ def plot_ctrl_dip_by_plate(df_controls, title=None, subtitle=None):
Title (or None to auto-generate)
subtitle: str, optional
Subtitle (or None to auto-generate)
template: str
Name of plotly template (https://plot.ly/python/templates/)
Returns
-------
Expand Down Expand Up @@ -1646,12 +1674,14 @@ def plot_ctrl_dip_by_plate(df_controls, title=None, subtitle=None):
))

layout = go.Layout(title=title,
template=template,
yaxis={'title': 'DIP Rate (h<sup>-1</sup>)'})
return go.Figure(data=traces, layout=layout)


def plot_plate_map(plate_data, color_by='dip_rates',
missing_color='lightgray', subtitle=None):
missing_color='lightgray', subtitle=None,
template=config.plotly_template):
"""
Parameters
Expand All @@ -1664,6 +1694,8 @@ def plot_plate_map(plate_data, color_by='dip_rates',
Color to use for missing values (default: lightgray)
subtitle: str or None
Subtitle, or None to auto-generate
template: str
Name of plotly template (https://plot.ly/python/templates/)
Returns
-------
Expand Down Expand Up @@ -1745,14 +1777,16 @@ def plot_plate_map(plate_data, color_by='dip_rates',
mode='text'
)

label_color = 'white' if template == 'plotly_dark' else 'black'

col_labels = go.Scatter(
x=[i + well_rad for i in range(cols)],
y=[rows + 1.2] * cols,
mode='text',
text=col_labels,
hoverinfo='none',
textfont=dict(
color='black',
color=label_color,
# size=18,
)
)
Expand All @@ -1764,7 +1798,7 @@ def plot_plate_map(plate_data, color_by='dip_rates',
text=row_labels,
hoverinfo='none',
textfont=dict(
color='black',
color=label_color,
# size=18,
)
)
Expand Down Expand Up @@ -1792,7 +1826,8 @@ def plot_plate_map(plate_data, color_by='dip_rates',
},
'hovermode': 'closest',
'showlegend': False,
'title': title
'title': title,
'template': template
})

return go.Figure(data=data, layout=layout)

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