plot topological relationship of two gene sets

Description

plot topological relationship of two gene sets (which are associated with two diseases respectively).

Usage

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plot_topo(geneset1, geneset2, graph, vertexcolor = c("tomato", "orange",
  "lightsteelblue"), vertex.shape = "circle", vertex.size = 14,
  vertex.label.font = 1, vertex.label.dist = 0,
  vertex.label.color = "black", vertex.label.cex = 0.5,
  edge.color = "black", layout = layout.auto)

Arguments

geneset1

a character vector contains gene ids

geneset2

another character vector contains gene ids

graph

an igraph graph object which represents a gene network

vertexcolor

a character vector contains 3 colors for vertexs

vertex.shape

vertex shape

vertex.size

vertex size

vertex.label.font

label text font

vertex.label.dist

label text dist

vertex.label.color

label text color

vertex.label.cex

label text cex

edge.color

edge color

layout

layout

Value

an igraph plot object

Author(s)

Peng Ni, Min Li

Examples

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data("PPI_HPRD")
g<-graph.data.frame(PPI_HPRD,directed = FALSE) #get an igraph graph 

data(d2g_fundo_symbol)
a<-d2g_fundo_symbol[["DOID:8242"]] # get gene set a
b<-d2g_fundo_symbol[["DOID:4914"]] # get gene set b

plot_topo(a,b,g)

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