ESEA (version 1.0)

PlotPathwayGraph: Plot the pathway-result network diagram

Description

Plot the pathway-result network diagram, the edges which contribute to the pathway enrichment score are marked with red.

Usage

PlotPathwayGraph(graph, margin = 0, vertex.label.cex = 0.6, vertex.label.font = 1,  vertex.size = 8, vertex.size2 = 6, vertex.shape = "rectangle", layout = layout.random, vertex.label.color = "black", edge.color = "dimgray", vertex.color = "#C1FFC1",  vertex.frame.color = "dimgray", axes = FALSE, xlab = "", ylab = "", sub = NULL,  main = NULL, ...)

Arguments

graph

A dataframe of pathway result obtained from the ESEA.main function

margin

A numeric. The value is usually between -0.5 and 0.5, which is able to zoom in or out a pathway graph. The default is 0.

vertex.label.cex

A numeric vector of node label size.

vertex.label.font

A numeric vector of label font.

vertex.size

A numeric vector of Node size. See plot.igraph

vertex.size2

A numeric vector of Node size.

vertex.shape

A vector of node shape. The default is graphics_type.

layout

A matrix of x-y coordinates with two dims. Determine the placement of the nodes for drawing a graph.The default is layout.random.

vertex.label.color

A vector of node label colors. The default is black.

vertex.color

A vector of node colors. The default is the KEGG node color.

vertex.frame.color

A vector of node frame color. The default is dimgray.

edge.color

A vector of edge color. The default is dimgray.

axes

A logical. whether to plot axes. The default is FALSE.

xlab

A character string. The label of the horizontal axis. The default is the empty string.

ylab

A character string. The label of the vertical axis. The default is the empty string.

sub

A character string of subtitle.

main

A character string of main title.

...

The arguments passed to or from methods. See plot.igraph and see plot.

Examples

## Not run: 
# 
# #get example data
# dataset<-GetExampleData("dataset")
# class.labels<-GetExampleData("class.labels")
# controlcharactor<-GetExampleData("controlcharactor")
# 
# #get the data for background set of edges
# edgesbackgrand<-GetEdgesBackgrandData()
# 
# #get the edge sets of pathways
# pathwayEdge.db<-GetPathwayEdgeData()
# 
# #calculate the differential correlation score for edges
# EdgeCorScore<-calEdgeCorScore(dataset, class.labels, controlcharactor,edgesbackgrand)
# 
# #identify dysregulated pathways by using the function ESEA.Main
# #Results<-ESEA.Main(EdgeCorScore,pathwayEdge.db)
# Results<-GetExampleData("PathwayResult")
# 
# #obtain the detail results of genes for a significant pathway
# PathwayNetwork<-Results[[2]][[1]]
# 
# #Plot the pathway-result network diagram, the edges which contribute to the ES are labeled with red.
# PlotPathwayGraph(PathwayNetwork,layout=layout.random)
# 
# ## End(Not run)