Plots
The plots package hosts plotting functions supported by Pyro-Velocity.
cluster_violin_plots
pyrovelocity.plots.cluster_violin_plots(data_model, adata, posterior_samples, cluster_key, violin_flag, pairs, show_outlier, fig_name=None)
Construct violin plots for each cluster.
extrapolate_prediction_sample_predictive
pyrovelocity.plots.extrapolate_prediction_sample_predictive(posterior_time, data_model_path, adata, grid_time_points=1000, use_gpu='cpu')
get_posterior_sample_angle_uncertainty
pyrovelocity.plots.get_posterior_sample_angle_uncertainty(posterior_angles)
plot_gene_ranking
pyrovelocity.plots.plot_gene_ranking(posterior_samples, adata, ax=None, time_correlation_with='s', selected_genes=None, assemble=False, negative=False, show_marginal_histograms=False, save_volcano_plot=False, volcano_plot_path='volcano.pdf')
plot_parameter_posterior_distributions
pyrovelocity.plots.plot_parameter_posterior_distributions(posterior_samples, adata, geneset, parameter_uncertainty_plot, parameter_names=['alpha', 'beta', 'gamma', 'u_offset', 's_offset', 't0'])
plot_posterior_time
pyrovelocity.plots.plot_posterior_time(posterior_samples, adata, ax=None, fig=None, basis='umap', addition=True, position='left', s=3)
plot_state_uncertainty
pyrovelocity.plots.plot_state_uncertainty(posterior_samples, adata, kde=True, data='denoised', top_percentile=0.9, ax=None, basis='umap')
plot_t0_selection
pyrovelocity.plots.plot_t0_selection(posterior_samples, t0_selection_plot)
Plot the t0, switching time, and cell time posterior samples.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
posterior_samples |
Dict[str, np.ndarray] | Dictionary of posterior samples. | required |
t0_selection_plot |
PathLike | str | Path to save the plot. | required |
Returns
| Type | Description |
|---|---|
| FigureBase | Matplotlib figure object. |
posterior_curve
pyrovelocity.plots.posterior_curve(adata, posterior_samples, gene_set, data_model, model_path, output_directory)
rainbowplot
pyrovelocity.plots.rainbowplot(volcano_data, adata, posterior_samples, fig=None, genes=None, data=['st', 'ut'], cell_state='clusters', basis='umap', num_genes=5, add_line=True, negative_correlation=False, scvelo_colors=False, save_plot=False, show_data=True, rainbow_plot_path='rainbow.pdf')
plot_vector_field_summary
pyrovelocity.plots.plot_vector_field_summary(adata, posterior_samples, vector_field_basis, plot_name, cell_state='cell_type')
plot_gene_selection_summary
pyrovelocity.plots.plot_gene_selection_summary(adata, posterior_samples, plot_name='', basis='', cell_state='', show_marginal_histograms=False, selected_genes=None)