Here is an example of how to highlight the members of a subgraph on a plot of a network graph.

## Load R libraries
library(igraph)

# Set adjacency matrix
g <- matrix(c(0,1,1,1, 1,0,1,0, 1,1,0,1, 0,0,1,0),nrow=4,ncol=4,byrow=TRUE)

# Set adjacency matrix to graph object
g <- graph.adjacency(g,mode="directed")

# Add node attribute label and name values
V(g)$name <- c("n1","n2","n3","n4")

# Set subgraph members
c <- c("n1","n2","n3")

# Add edge attribute id values
E(g)$id <- seq(ecount(g))

# Extract supgraph
ccsg <- induced.subgraph(graph=g,vids=c)

# Extract edge attribute id values of subgraph
ccsgId <- E(ccsg)$id

# Set graph and subgraph edge and node colors and sizes
E(g)$color="grey"
E(g)$width=2
E(g)$arrow.size=1
E(g)$arrow.width=1
E(g)[ccsgId]$color <- "#DC143C" # Crimson
E(g)[ccsgId]$width <- 2
V(g)$size <- 4
V(g)$color="#00FFFF" # Cyan
V(g)$label.color="#00FFFF" # Cyan
V(g)$label.cex <-1.5
V(g)[c]$label.color <- "#DC143C" # Crimson
V(g)[c]$color <- "#DC143C" # Crimson

# Set seed value
set.seed(40041)

# Set layout options
l <- layout.fruchterman.reingold(g)

# Plot graph and subgraph
plot.igraph(x=g,layout=l)

Simple, no?