How to Plot Igraph Community with Defined Colors

How can I plot igraph community with defined colors?

Yes, you can do both of those things. Changing the colors of the nodes according to which module they are in (as well as changing the colors of the polygons around the modules) is straightforward using arguments in plot.igraph. Adding text to modules is not so trivial, and the easiest solution is as far as I know is to add text to the plot manually.

library(igraph)

# Generate random graph and community structure
set.seed(23)
g <- sample_gnm(15, 45)
wc <- walktrap.community(g)

# Plot
par(mfrow=c(1,2), mar=rep(1,4))
layout <-layout.fruchterman.reingold(g)
plot(wc, g, layout=layout, vertex.label=NA, vertex.size=5,  edge.arrow.size=.2)

# Change colors of nodes, polygons, and polygon borders
new_cols <- c("white", "red", "black")[membership(wc)]
plot(wc, g, col=new_cols, mark.border="black", mark.col=c("tan", "pink", "lightgray"), 
    layout=layout, vertex.label=NA, vertex.size=5, edge.arrow.size=.2)

# Add labels
text(c(-1.15, 0.8, 0.9), c(0.35, -0.7, 0.8), c("A", "B", "C"))

How can I plot igraph community with colors according to attributes?

What you tried to set the vertex color vertex.color=V(g)$att makes sense, but unfortunately does not work when plotting communities. Instead, use col=V(g)$att to set the vertex color. If you need to change the color for the polygons, use mark.color.

plot(wc, g, layout=layout, vertex.label=NA, mark.col=rainbow(5, alpha=0.3),
    vertex.size=10, col=V(g)$att,  edge.arrow.size=.2)

Individual coloring of single communities

Identify the vertices in each group > 1 and pass those as a list to mark.groups. It is a bit fiddly, but it works.

r <- rle(sort(communities$membership))
x <- r$values[which(r$lengths>1)]
y <- r$values[which(r$lengths==1)]
cols <- communities$membership
cols[which(cols %in% y)] <- "white"
grps <- lapply(x, function(x) communities[[x]])
grps <- lapply(1:length(grps), function(x) which(V(g)$name %in% grps[[x]]))
plot(communities, trimmed_network, layout=network_layout, 
 col = cols, mark.groups = grps)

How to colour edges within community clusters in igraph

The following should work:

library(igraph)
g <- watts.strogatz.game(1, 100, 5, 0.05)
clp <- cluster_label_prop(g)
V(g)$community <- clp$membership
rain <- rainbow(14, alpha=.5)
V(g)$color <- rain[V(g)$community]

E(g)$color <- apply(as.data.frame(get.edgelist(g)), 1, 
                function(x) ifelse(V(g)$community[x[1]] == V(g)$community[x[2]], 
                                   rain[V(g)$community[x[1]]], '#00000000'))
plot(g, vertex.size=4, vertex.label=NA, edge.color=E(g)$color)

Control of colors in complex network graph using igraph

For the clusters highlight:

plot(cfg,g, mark.col=c("red","green"))

r igraph - plot communies and selectively highlight some

I think that you mean that you do not want the polygon around group 2. You can get this effect by setting the mark.border and the mark.col to NA.

plot(wctemp, temp, col=new_cols, mark.border=c("black", NA, "black"), 
     mark.col=c("tan", NA, "lightgray"), 
     layout=layout, vertex.label=NA, vertex.size=5, edge.arrow.size=.2)

Addition:

Based on the comments, I gather that you have a list of clusters to highlight and want to work from that list. Just pick a point color for "not highlighted" (I used "darkgray") and make the polygon colors be NA except for the highlighted communities.

ToHighlight = c(1,3)

PCol = rep("darkgray", length(unique(wctemp$membership)))
PCol[ToHighlight] = rainbow(length(ToHighlight))
new_cols <- PCol[membership(wctemp)]

HCol = rep(NA, length(unique(wctemp$membership)))
HCol[ToHighlight] = rainbow(length(ToHighlight), alpha=0.15)

plot(wctemp, temp, col=new_cols, mark.border=HCol, mark.col=HCol, 
     layout=layout, vertex.label=NA, vertex.size=5, edge.arrow.size=.2)

Assign colour to chosen communities in a plot

I had to tweak your adjacency matrix so that more than 1 community showed up.

library(igraph)
ob <- read.table(text="
    A   B   C   D   E   F   G
A   0   1   0   1   0   1   0
B   1   0   1   1   0   1   0
C   0   0   0   0   0   0   0
D   1   1   0   0   1   0   0
E   0   0   0   1   0   1   1
F   0   1   0   0   1   0   1
G   0   0   0   0   1   1   0", header=TRUE)

m <- as.matrix(ob)
g <- graph.adjacency(m, mode="undirected", weighted = T, add.rownames = T)
com <- edge.betweenness.community(g)
V(g)$memb <- com$membership

cols <- membership(com)  
cols[cols!=3] <- 1

plot(g, vertex.color=cols)

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