plotSub: Plot of the subnetwork

In leiming8886/fRNC: ncRNA module search functions

Plot of the subnetwork

Description

The function plots a network from graphNEL or igraph format. It is used to visualize the modules. For further plotting options use the plot.igraph function of the igraph package. The shapes of the nodes can be changed according to the scores argument, then negative scores appear squared The color of the nodes can be changed according to the diff.expr argument. Negative(positive) values lead to green(red) nodes.

Usage

plotSub(
  network,
  layout = layout.fruchterman.reingold,
  labels = NULL,
  diff.expr = NULL,
  scores = NULL,
  main = NULL,
  vertex.size = NULL
)

Arguments

network	A graph in igraph or graphNEL format.
layout	Layout algorithm, e.g. layout.fruchterman.reingold or layout.kamada.kawai.
labels	Labels for the nodes of the network
diff.expr	Named numerical vector of log2FC of the nodes in the network for coloring of the nodes.
scores	Named numerical vector of scores of the nodes for the shape of the node in the network.
main	Main title of the plot.
vertex.size	Numerical value or verctor for the size of the vertices.

References

Daniela Beisser, Gunnar W. Klau, Thomas Dandekar et al. (2010) BioNet: an R-Package for the functional analysis of biological networks

Examples

library(igraph)
edgel <- cbind(c("1", "2", "3", "4", "5", "6", "7"),
c("b", "c", "d", "e", "f", "a", "b"))
g <- graph.edgelist(edgel, directed=TRUE)
V(g)$type <- c(rep("lncRNA",4),rep("miRNA",4),rep("circRNA",5))
plotSub(g)

leiming8886/fRNC documentation built on Feb. 21, 2023, 4:12 p.m.