plotGraph(graph,margin=0,vertex.label.cex=0.6,vertex.label.font=1, vertex.size=8,vertex.size2=6,edge.arrow.size=0.2, edge.arrow.width=3,vertex.label=V(graph)$graphics_name, vertex.shape=V(graph)$graphics_type,layout=getLayout(graph), vertex.label.color="black",vertex.color=V(graph)$graphics_bgcolor, vertex.frame.color="dimgray",edge.color="dimgray", edge.label=getEdgeLabel(graph),edge.label.cex=0.6, edge.label.color="dimgray",edge.lty=getEdgeLty(graph), axes=FALSE,xlab="",ylab="",sub=NULL,main=NULL,...)
plot.igraph
plot
.plotGraph
is able to display a pathway graph. The argument layout
is used to determine the placement of the nodes for drawing a graph. There are mainly two preprocessed methods to determine the placement of the nodes for drawing a pathway graph: the KEGG pathway layout and layout
provided in the function plot.igraph
of the igraph
package. The default layout is the KEGG layout, for which the coordinates of nodes in KEGG is used to determine the placement of the nodes for drawing a graph. Therefore, the returned figure by the function may be very similar to the KEGG pathway graph when information in the pathway graph is complete relatively. The layouts provided in igraph
include layout.reingold.tilford
, layout.random
, layout.circle
, layout.sphere
,..., .
plot
, layout.random
## Not run:
# ### get metabolic pathway graphs ###
#
# g<- GetK2riData(K2riData="MetabolicGEGEEMGraph")
#
# # visualize the graph
# plotGraph(g[[1]],layout=layout.random)
#
# ## End(Not run)
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