Re: [igraph] Need help with plotting

[Gábor Csárdi]

I guess the problem is that edge.betweenness.community interprets edge weights the opposite way. Small numbers mean short links, so strong connections. Use 1 / weights, maybe?

Gabor

On Mon, Dec 7, 2015 at 4:39 PM, Raj Balakrishnan <address@hidden> wrote:

Dear Gabor,

Isn't the example I have included enough?

Thanks,

Raj

Raj Balakrishnan
--------------------------------
Sent from my mobile phone

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From: Gábor Csárdi
Sent: ‎07-‎12-‎2015 07:26
To: Help for igraph users
Subject: Re: [igraph] Need help with plotting

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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