Hierarchical plot of biological network

Share:

Description

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

Usage

1
2
3
4
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

1
2
3
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")

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.