Re: [igraph] Need help with plotting

[Gábor Csárdi]

I am not sure what is going on here? Are you saying that edge.betweenness.community is buggy? Possibly, but then please show us why on some small example?

Gabor

On Mon, Dec 7, 2015 at 2:40 PM, Rk Lata <address@hidden> wrote:

Hi there,

I am trying to plot self and cross reactions of bunch of proteins. I have three states: Positive=1, Negative=0 and Partial=0.5. When I plot the values in the matrix using the code below, I get the plot shown in Fig A. I am expecting a plot as in Fig B. (Please see the Figures attached). 

What should I do to make the weakly self reacting proteins (c & d) appear as a separate group and not in group with other  strongly self reacting proteins. 

	a	b	c	d	e	f	g	h	i
a	1	0	0	0	0	0	0	0	0
b	0	1	1	0	0	0	0	0	0
c	0	0	0.5	0	0	0	0	0	0
d	0	0	0	0.5	0	0	0	0	0
e	0	0	0	1	1	1	1	0	0
f	0	0	0	0	1	1	1	0	0
g	0	0	0	0	1	1	1	0	0
h	0	0	0	0	0	0	0	1	1
i	0	0	0	0	0	0	0	1	1

m <- as.matrix(read.csv("C:/Users/balakrr1/Desktop/csv/n3.csv", header=TRUE, sep = ",", row.names = 1))

g = graph.adjacency(m,mode="undirected",weighted=TRUE)

g=simplify(g, remove.loops=TRUE)

eb=edge.betweenness.community(g,directed=FALSE,weights=E(g)$weight)

fr=layout.fruchterman.reingold(g)

plot(eb,g,layout=fr,edge.width=E(g)$weight,main="Edge Betweenness")

Thanks,

Raj

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