plot_topo {dSimer} | R Documentation

## plot topological relationship of two gene sets

### 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)

[Package dSimer version 1.12.0 Index]