plot_topo: plot topological relationship of two gene sets

In dSimer: Integration of Disease Similarity Methods

Description

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

Usage

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

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)

dSimer documentation built on May 2, 2019, 12:40 a.m.