plot_bipartite: plot disease-gene (or GO term etc.) associations as a...

In PengNi/dSimer: Integration of Disease Similarity Methods

Description

plot a bipartite graph which visualizes associations between diseases and genes (or GO terms etc.)

Usage

plot_bipartite(xylist, vertex.size = 12, vertex.shape1 = "circle",
  vertex.shape2 = "square", vertex.color1 = "darkseagreen",
  vertex.color2 = "turquoise1", vertex.label.font = 2,
  vertex.label.dist = 0, vertex.label.color = "black",
  vertex.label.cex = 0.8, edge.color = "black",
  layout = layout.kamada.kawai)

Arguments

xylist	a named list object which names are diseases and each element of the list is a gene set with respect to each disease.
vertex.size	vertex size
vertex.shape1	shape for one kind of vertex
vertex.shape2	shape for another kind of vertex
vertex.color1	color for one kind of vertex
vertex.color2	color for another kind of vertex
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(d2g_fundo_symbol)
d2g_sample<-sample(d2g_fundo_symbol, 3)
plot_bipartite(d2g_sample)

PengNi/dSimer documentation built on May 8, 2019, 1:28 a.m.