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 <[email protected]> wrote: > Dear Gabor, > > Isn't the example I have included enough? > > Thanks, > > Raj > > Raj Balakrishnan > -------------------------------- > Sent from my mobile phone > ------------------------------ > From: Gábor Csárdi <[email protected]> > Sent: 07-12-2015 07:26 > To: Help for igraph users <[email protected]> > 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 <[email protected]> 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. >> >> >> abcdefghia100000000b011000000c000.5000000d0000.500000e000111100f000011100 >> g000011100h000000011i000000011 >> >> 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 >> >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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