Visualize

pyggdrasil.visualize.plot_tree(tree, save_name, save_dir, print_options, rename_labels=None)

Plot a tree and save it to a file.

Parameters:

Name	Type	Description	Default
tree	TreeNode	TreeNode tree to plot, given the root node tree.data: may contain info to print for tree / node e.g. "log-likelihood": float likelihood of the tree tree.name: name of tree, may use a title of plot	required
save_name	str	str name of the file to save the plot to	required
save_dir	Path	Path directory to save the plot to	required
print_options	dict	dict options for printing the tree "title": bool whether to print the name/title of the tree/root "data_tree": dict what attributes to print of the tree	required
rename_labels	Optional[dict[str, NodeLabel]]	dict dictionary of labels to rename {0:1, 1:2, 3:"IPC4", 4:"IPC5"} {old_label:new_label, ...} pass empty dict to not rename labels	None

Returns: None

Note

see tests/visualize/test_tree.py for example usage

pyggdrasil.visualize.save_metric_iteration(iteration, distances, metric_name, out_fp)

Save plot of distance to true tree vs iteration number to disk.

Parameters:

Name	Type	Description	Default
iteration	list[int]	list[int] Iteration numbers, 1-indexed.	required
out_fp	Path	Path Output file path.	required
distances	list[float]	ndarray Distances to true tree for each iteration.	required
metric_name	str	str Name of distance metric.	required

pyggdrasil.visualize.save_log_p_iteration(iterations, log_probs, output_fp)

Save plot of log probability vs iteration number to disk.

Parameters:

Name	Type	Description	Default
output_dir		Path Output directory to save the plot.	required
iterations	list[int]	list[int] Iteration numbers, 1-indexed.	required
log_probs	list[float]	list[float] Log probabilities.	required

pyggdrasil.visualize.plot_tree_mcmc_sample(sample, save_dir, save_name='')

Takes input of get_sample of PureMcmcData and , Plot a tree and save it to a file with just its iteration number and log probability, in the savename.

pyggdrasil.visualize.plot_tree_no_print(tree, save_name, save_dir)

Takes input of get_sample of PureMcmcData and , Plot a tree and save it to a file with just its iteration number and log probability, in the savename.

pyggdrasil.visualize.save_top_trees_plots(data, output_dir)

Save plots of top three trees by log probability to disk, with accompanying json to node the iterations.

Parameters:

Name	Type	Description	Default
data		mcmc samples	required
output_dir		path to output directory	required

Returns:

Type	Description
None	None

Saves

top_tree_1.svg top_tree_2.svg top_tree_3.svg top_trees_iterations.json

pyggdrasil.visualize.save_rhat_iteration(iteration, rhats, out_fp)

Save plot of rhat vs iteration number to disk.

Parameters:

Name	Type	Description	Default
iteration	list[int]	list[int] Iteration numbers.	required
out_fp	Path	Path Output file path.	required
rhats	list[float]	ndarray R hat values for each iteration.	required

pyggdrasil.visualize.save_rhat_iteration_AD_DL(iteration, rhats_AD, rhats_DL, out_fp)

Save plot of rhat vs iteration number to disk.

Parameters:

Name	Type	Description	Default
iteration	list[int]	list[int] Iteration numbers.	required
out_fp	Path	Path Output file path.	required
rhats_AD	list[float]	ndarray R hat values for each iteration for AD.	required
rhats_DL	list[float]	ndarray R hat values for each iteration for DL.	required

pyggdrasil.visualize.save_ess_iteration_AD_DL(iteration, ess_bulk_AD, ess_bulk_DL, ess_tail_AD, ess_tail_DL, out_fp)

Save plot of ess vs iteration number to disk.

Parameters:

Name	Type	Description	Default
iteration	list[int]	list[int] Iteration numbers.	required
out_fp	Path	Path Output file path.	required
TODO		add description	required