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.
abcdefghia100000000b011000000c000.5000000d0000.500000e000111100f000011100g00
0011100h000000011i000000011
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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