Plots and visualization (thunor.plots
)¶
-
exception
thunor.plots.
CannotPlotError
¶
-
thunor.plots.
plot_ctrl_cell_counts_by_plate
(df_controls, title=None, subtitle=None, template='none')¶ - Parameters
df_controls (pd.DataFrame) – Control well cell counts
title (str, optional) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
-
thunor.plots.
plot_ctrl_dip_by_plate
(df_controls, title=None, subtitle=None, template='none')¶ - Parameters
df_controls (pd.DataFrame) – Control well DIP values
title (str, optional) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
-
thunor.plots.
plot_drc
(fit_params, is_absolute=False, color_by=None, color_groups=None, title=None, subtitle=None, template='none')¶ Plot dose response curve fits
- Parameters
fit_params (pd.DataFrame) – Fit parameters from
thunor.curve_fit.fit_params()
is_absolute (bool) – For DIP rate plots, use absolute (True) or relative (False) y-axis scale. Ignored for viability plots.
color_by (str or None) – Color the traces by cell lines if ‘cl’, drugs if ‘dr’, or arbitrarily if None (default)
color_groups (dict or None) – If using color_by, provide a dictionary containing the color groups, where the values are cell line or drug names
title (str, optional) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
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thunor.plots.
plot_drc_params
(df_params, fit_param, fit_param_compare=None, fit_param_sort=None, title=None, subtitle=None, aggregate_cell_lines=False, aggregate_drugs=False, multi_dataset=False, color_by=None, color_groups=None, template='none', **kwargs)¶ Box, bar, or scatter plots of DIP rate fit parameters
- Parameters
df_params (pd.DataFrame) – DIP fit parameters from
thunor.dip.dip_params()
fit_param (str) – Fit parameter name, e.g. ‘ic50’
fit_param_compare (str, optional) – Second fit parameter name for comparative plots, e.g. ‘ec50’
fit_param_sort (str, optional) – Fit parameter name to use for sorting the x-axis, if different from fit_param
title (str, optional) – Title (or None to auto-generate)
subtitle (str, optional) – Subtitle (or None to auto-generate)
aggregate_cell_lines (bool or dict, optional) – Aggregate all cell lines (if True), or aggregate by the specified groups (dict of cell line names as values, with group labels as keys)
aggregate_drugs (bool or dict, optional) – Aggregate all drugs (if True), or aggregate by the specified groups (dict of drug names as values, with group labels as keys)
multi_dataset (bool) – Set to true to compare two datasets contained in fit_params
color_by (str or None) – Color by cell lines if “cl”, drugs if “dr”, or arbitrarily if None (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
- Returns
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
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thunor.plots.
plot_drug_combination_heatmap
(ctrl_resp_data, expt_resp_data, title=None, subtitle=None, template='none')¶ Plot heatmap of drug combination response by DIP rate
Two dimensional plot (each dimension is a drug concentration) where squares are coloured by DIP rate value.
- Parameters
ctrl_resp_data (pd.DataFrame) – Control DIP rates from
thunor.dip.dip_rates()
expt_resp_data (pd.DataFrame) – Experiment (non-control) DIP rates from
thunor.dip.dip_rates()
title (str, optional) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
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thunor.plots.
plot_plate_map
(plate_data, color_by='dip_rates', missing_color='lightgray', subtitle=None, template='none')¶ - Parameters
plate_data (thunor.io.PlateData) – Plate map layout data
color_by (str) – Attribute to color wells by, must be numerical (default: dip_rates)
missing_color (str) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
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thunor.plots.
plot_time_course
(hts_pandas, log_yaxis=False, assay_name='Assay', title=None, subtitle=None, show_dip_fit=False, template='none')¶ Plot a dose response time course
- Parameters
hts_pandas (HtsPandas) – Dataset containing a single cell line/drug combination
log_yaxis (bool) – Use log scale on y-axis
assay_name (str) – The name of the assay to use for the time course (only used for multi-assay datasets)
title (str, optional) – Title (or None to auto-generate)
subtitle (str, optional) – 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
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure
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thunor.plots.
plot_two_dataset_param_scatter
(df_params, fit_param, title, subtitle, color_by, color_groups, template='none', **kwargs)¶ Plot a parameter comparison across two datasets
- Parameters
df_params (pd.DataFrame) – DIP fit parameters from
thunor.dip.dip_params()
fit_param (str) – The name of the parameter to compare across datasets, e.g. ic50
title (str, optional) – 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
- Returns
A plotly figure object containing the graph
- Return type
plotly.graph_objs.Figure