location: Hierarchical plot of biological network

In ProNet: Biological Network Construction, Visualization and Analyses

Description

Hierarchical plot of biological network according to the elements' subcellular location.

Usage

location(graph, species = c("human", "ath"), vertex.color = 1,
  vertex.size = 10, vertex.shape = "square", edge.color = 1,
  label.add = TRUE, colorbar.add = TRUE, xlim = c(-1, 1), ylim = c(-1,
  1), ...)

Arguments

graph	An igraph object.
species	The species name, currently only human and ath are available.
vertex.color	Color of the vertex. Default value is 1.
vertex.size	Size of the vertex. Default value is 10.
vertex.shape	Shape of the vertex. Default value is square.
edge.color	Color of the edge. Default value is 1.
label.add	Boolean value, whether to add label to the plot (if TRUE) or not (if FALSE).
colorbar.add	Boolean value, whether to add colorbar to the plot (if TRUE) or not (if FALSE).
xlim	A vector indicating the range of x axis.
ylim	A vector indicating the range of y axis.
...	Other arguments.

Value

A hierarchical plot of biological network.

References

Barsky A, Gardy JL, Hancock REW, and Munzner T. (2007) Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 23(8):1040-2.

Examples

gene<-data.frame(c("DVL1","DVL2","DVL3"))
net<-construction(input=gene,db="HPRD",species="human",ID.type="Gene symbol",hierarchy=1)
location(net,species="human",vertex.color="vertex.hierarchy")

ProNet documentation built on May 30, 2017, 2:02 a.m.