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.
Author(s)
Junwei Han <hanjunwei1981@163.com>, Xinrui Shi<xinrui103@163.com> and Chunquan Li <lcqbio@163.com>
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)