Functions to write spatiotemporal graph information to files. More...

Detailed Description

Functions to write spatiotemporal graph information to files.

Functions
def	draw_dag
	Function to render the DAG with heatmap information. More...

def	draw_dag_in_graphviz
	Draw a DAG representation in graphviz and return the resulting Digraph. More...

def	write_cdf
	Function to output the cumulative distribution function (cdf) More...

def	write_final_npaths
	Function to output a file with all states for each of the n most likely paths. More...

def	write_labeled_pdf
	Function to output the labeled probability distribution function (pdf) More...

def	write_pdf
	Function to output the probability distribution function (pdf) More...

Function Documentation

def IMP.spatiotemporal.write_output.draw_dag	(	dag_fn,
		nodes,
		paths,
		path_prob,
		keys,
		heatmap = `True`,
		colormap = `'Purples'`,
		penscale = `0.6`,
		arrowsize = `1.2`,
		fontname = `'Helvetica'`,
		fontsize = `'18'`,
		height = `'0.6'`,
		width = `'0.6'`,
		draw_label = `True`
	)

Function to render the DAG with heatmap information.

Parameters

dag_fn	string, filename path
nodes	list of graphNode objects for which the graph will be drawn
paths	list of lists containing all paths visited by the graphNode objects
path_prob	list of probabilities for each path, (path_prob from score_graph())
keys	states visited in the graph (list of keys to the state_dict)
heatmap	Boolean to determine whether or not to write the dag with a heatmap based on the probability of each state (default: True)
colormap	string, colormap used by the dag to represent probability. Chooses from those available in matplotlib (https://matplotlib.org/stable/users/explain/colors/colormaps.html) (default: "Purples").
penscale	float, size of the pen used to draw arrows on the dag
arrowsize	float, size of arrows connecting states on the dag
fontname	string, font used for the labels on the dag
fontsize	string, font size used for the labels on the dag
height	string, height of each node on the dag
width	string, width of each node on the dag
draw_label	Boolean to determine whether or not to draw state labels on the dag

Note: This function is only available in Python.

Definition at line 169 of file write_output.py.

def IMP.spatiotemporal.write_output.draw_dag_in_graphviz	(	nodes,
		coloring = `None`,
		draw_label = `True`,
		fontname = `'Helvetica'`,
		fontsize = `'18'`,
		penscale = `0.6`,
		arrowsize = `1.2`,
		height = `'0.6'`,
		width = `'0.6'`
	)

Draw a DAG representation in graphviz and return the resulting Digraph.

Takes a list of graphNodes and initializes the nodes and edges. Coloring is expected to be a list of RGBA strings specifying how to color each node. Expected to be same length as nodes.

Parameters

nodes	list of graphNode objects
coloring	list of RGBA strings to specify the color of each node. Expected to be the same length as nodes
draw_label	bool, whether or not to draw graph labels
fontname	string, name of font for graph labels
fontsize	string, size of font for graph labels
penscale	float, size of pen
arrowsize	float, size of arrows
height	string, height of nodes
width	string, width of nodes

Returns: dot: Digraph object to be rendered

Note: This function is only available in Python.

Definition at line 110 of file write_output.py.

def IMP.spatiotemporal.write_output.write_cdf	(	out_cdf,
		cdf_fn,
		graph_prob
	)

Function to output the cumulative distribution function (cdf)

Parameters

out_cdf	bool, writes cdf if true
cdf_fn	str, filename of cdf
graph_prob	list of probabilities for each path, (path_prob from score_graph())

Note: This function is only available in Python.

Definition at line 23 of file write_output.py.

def IMP.spatiotemporal.write_output.write_final_npaths	(	npaths,
		npath_fn,
		graph_scores,
		graph_prob
	)

Function to output a file with all states for each of the n most likely paths.

Parameters

npaths	int, number of paths to output
npath_fn	str, name of the file for all paths
graph_scores	list of tuples, where the first object is the path (list of graphNode objects for each state along the trajectory), and the second object is the score of the path, which can be used to calculate the probability. (path_scores from score_graph())
graph_prob	list of probabilities for each path, (path_prob from score_graph())

Note: This function is only available in Python.

Definition at line 78 of file write_output.py.

def IMP.spatiotemporal.write_output.write_labeled_pdf	(	out_labeled_pdf,
		labeled_pdf_fn,
		graph,
		graph_prob
	)

Function to output the labeled probability distribution function (pdf)

Parameters

out_labeled_pdf	bool, writes labeled_pdf if true
labeled_pdf_fn	str, filename of labeled_pdf
graph	list of graphNode objects visited for each path, (all_paths from score_graph())
graph_prob	list of probabilities for each path, (path_prob from score_graph())

Note: This function is only available in Python.

Definition at line 50 of file write_output.py.

def IMP.spatiotemporal.write_output.write_pdf	(	out_pdf,
		pdf_fn,
		graph_prob
	)

Function to output the probability distribution function (pdf)

Parameters

out_pdf	bool, writes pdf if true
pdf_fn	str, filename of pdf
graph_prob	list of probabilities for each path, (path_prob from score_graph())

Note: This function is only available in Python.

Definition at line 37 of file write_output.py.