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Re: [igraph] Need help with plotting


From: Raj Balakrishnan
Subject: Re: [igraph] Need help with plotting
Date: Mon, 7 Dec 2015 08:39:17 -0800

Dear Gabor,

Isn't the example I have included enough?

Thanks,

Raj

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

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. 


abcdefghi
a100000000
b011000000
c000.5000000
d0000.500000
e000111100
f000011100
g000011100
h000000011
i000000011


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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