plotPathCluster: Plots the structure of specified path cluster

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Plots the structure of specified path cluster

Description

Plots the structure of specified path found by pathCluster.

Usage

plotPathCluster(ybinpaths, clusters, m, tol = NULL)

Arguments

ybinpaths	The training paths computed by pathsToBinary.
clusters	The pathway cluster model trained by pathCluster or pathClassifier.
m	The path cluster to view.
tol	A tolerance for 3M parameter theta which is the probability for each edge within each cluster. If the tolerance is set all edges with a theta below that tolerance will be removed from the plot.

Value

Produces a plot of the paths with the path probabilities and cluster membership probabilities.

Center Plot	An image of all paths the training dataset. Rows are the paths and columns are the genes (features) included within each path.
Right	The training set posterior probabilities for each path belonging to the current 3M component.
Top Bar Plots	Theta, The 3M component probabilities - indicates the importance of each edge to a pathway.

Author(s)

Timothy Hancock and Ichigaku Takigawa

See Also

Other Path clustering & classification methods: pathClassifier(), pathCluster(), pathsToBinary(), plotClassifierROC(), plotClusterMatrix(), plotPathClassifier(), predictPathClassifier(), predictPathCluster()

Examples

	## Prepare a weighted reaction network.
	## Conver a metabolic network to a reaction network.
 data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
 rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)

	## Assign edge weights based on Affymetrix attributes and microarray dataset.
 # Calculate Pearson's correlation.
	data(ex_microarray)	# Part of ALL dataset.
	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
		weight.method = "cor", use.attr="miriam.uniprot", bootstrap = FALSE)

	## Get ranked paths using probabilistic shortest paths.
 ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
					K=20, minPathSize=8)

	## Convert paths to binary matrix.
	ybinpaths <- pathsToBinary(ranked.p)
	p.cluster <- pathCluster(ybinpaths, M=2)
	plotPathCluster(ybinpaths, p.cluster, m=2, tol=0.05)

ahmohamed/NetPathMiner documentation built on Nov. 30, 2024, 1:18 a.m.