Plots an annotated igraph object higlighting ranked paths.

Description

This function plots a network highlighting ranked paths. If path.clusters are provided, paths in the same cluster are assigned similar colors.

Usage

plotPaths(paths, graph, path.clusters = NULL, col.palette = palette(),
  layout = layout.auto, ...)

Arguments

col.palette=rainbow

Value

Produces a plot of the network with paths highlighted. If paths are computed for several labels (sample categories), a plot is created for each label.

Author(s)

Ahmed Mohamed

See Also

Other Plotting methods: colorVertexByAttr; layoutVertexByAttr; plotAllNetworks; plotClassifierROC; plotClusterMatrix, plotClusterProbs, plotClusters; plotCytoscape, plotCytoscapeGML; plotNetwork; plotPathClassifier

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",
		y=factor(colnames(ex_microarray)), bootstrap = FALSE)

	## Get ranked paths using probabilistic shortest paths.
 ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
					K=20, minPathSize=6)

	## Plot paths.
	plotPaths(ranked.p, rgraph)

	## Convert paths to binary matrix, build a classifier.
	ybinpaths <- pathsToBinary(ranked.p)
	p.class <- pathClassifier(ybinpaths, target.class = "BCR/ABL", M = 3)

 ## Plotting with clusters, on a metabolic graph.
	plotPaths(ranked.p, ex_sbml, path.clusters=p.class)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NetPathMiner)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NetPathMiner/plotPaths.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPaths
> ### Title: Plots an annotated igraph object higlighting ranked paths.
> ### Aliases: plotPaths
> 
> ### ** 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",
+ 		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
100 genes were present in the microarray, but not represented in the network.
55 genes were couldn't be found in microarray.
Assigning edge weights for label ALL1/AF4 
Assigning edge weights for label BCR/ABL 
Assigning edge weights for label E2A/PBX1 
Assigning edge weights for label NEG 
> 
> 	## Get ranked paths using probabilistic shortest paths.
>  ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
+ 					K=20, minPathSize=6)
Extracting the 20 most probable paths for ALL1/AF4
Extracting the 20 most probable paths for BCR/ABL
Extracting the 20 most probable paths for E2A/PBX1
Extracting the 20 most probable paths for NEG
> 
> 	## Plot paths.
> 	plotPaths(ranked.p, rgraph)
> 
> 	## Convert paths to binary matrix, build a classifier.
> 	ybinpaths <- pathsToBinary(ranked.p)
> 	p.class <- pathClassifier(ybinpaths, target.class = "BCR/ABL", M = 3)
> 
>  ## Plotting with clusters, on a metabolic graph.
> 	plotPaths(ranked.p, ex_sbml, path.clusters=p.class)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>