PlotPathwayGraph: Plot the pathway-result network diagram

In hanjunwei-lab/ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

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.

Author(s)

Junwei Han <[e-mail]>, Xinrui Shi<[e-mail]> and Chunquan Li <[e-mail]>

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)

hanjunwei-lab/ESEA documentation built on July 5, 2020, 11:01 a.m.