Re: [igraph] Need help with plotting

[Rk Lata]

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

figA.JPG
Description: JPEG image

figB.JPG
Description: JPEG image