Maybe read ?igraph.plotting, that lists all graphical parameters. E.g. to set the width of an edge, so something like
plot(gg, edge.width=E(gg)$R2*5) Gabor On Thu, Nov 14, 2013 at 3:53 PM, Hermann Norpois <[email protected]> wrote: > Hello, > > > I just beginn to use igraph and I am really impressed. I was successful to > create an igraph object zu.network (see dput (zu.network)) from zu. I am > interested to display how the SNPs of SNP_A and SNP_B are connected with > respect to their position and R2. > > I started with > plot (zu.network) > but I was not able to find the syntax that satiesfies my needs. > > 1) How can I position the SNP_A with respect to position (position of > SNP_A). > 2) How can I display the strengh of the connection (expressed by R2) by > the thickness of the connecting line? > > Thanks > Hermann > > > > zu > SNP_A SNP_B R2 position > 2 rs4822747 rs4820690 0.695642 27001689 > 3 rs4822747 rs5761627 0.695642 27001689 > 4 rs4822747 rs5752355 0.687861 27001689 > 5 rs4822747 rs4822748 0.682715 27001689 > 6 rs4822747 rs4820691 0.695642 27001689 > 7 rs4822747 rs4822749 0.695642 27001689 > 9 rs4820690 rs4822747 0.695642 27002392 > 11 rs4820690 rs5761627 1.000000 27002392 > 12 rs4820690 rs5752355 0.988681 27002392 > 13 rs4820690 rs4822748 0.988655 27002392 > 14 rs4820690 rs4820691 1.000000 27002392 > 15 rs4820690 rs4822749 1.000000 27002392 > 16 rs4820690 rs4822750 0.988655 27002392 > 17 rs4820690 rs5761629 0.695642 27002392 > 19 rs5761627 rs4822747 0.695642 27004298 > 20 rs5761627 rs4820690 1.000000 27004298 > 22 rs5761627 rs5752355 0.988681 27004298 > 23 rs5761627 rs4822748 0.988655 27004298 > 24 rs5761627 rs4820691 1.000000 27004298 > 25 rs5761627 rs4822749 1.000000 27004298 > > > dput (zu.network) > structure(list(9, TRUE, c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, > 1, 1, 2, 2, 2, 2, 2, 2), c(1, 2, 3, 4, 5, 6, 0, 2, 3, 4, 5, 6, > 7, 8, 0, 1, 3, 4, 5, 6), c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, > 11, 12, 13, 14, 15, 16, 17, 18, 19), c(6, 14, 0, 15, 1, 7, 2, > 8, 16, 3, 9, 17, 4, 10, 18, 5, 11, 19, 12, 13), c(0, 6, 14, 20, > 20, 20, 20, 20, 20, 20), c(0, 2, 4, 6, 9, 12, 15, 18, 19, 20), > list(c(1, 0, 1), structure(list(), .Names = character(0)), > structure(list(name = c("rs4822747", "rs4820690", "rs5761627", > "rs5752355", "rs4822748", "rs4820691", "rs4822749", "rs4822750", > "rs5761629")), .Names = "name"), structure(list(R2 = c(0.695642, > 0.695642, 0.687861, 0.682715, 0.695642, 0.695642, 0.695642, > 1, 0.988681, 0.988655, 1, 1, 0.988655, 0.695642, 0.695642, > 1, 0.988681, 0.988655, 1, 1), position = c(27001689L, > 27001689L, 27001689L, 27001689L, 27001689L, 27001689L, > 27002392L, 27002392L, 27002392L, 27002392L, 27002392L, > 27002392L, 27002392L, 27002392L, 27004298L, 27004298L, > 27004298L, 27004298L, 27004298L, 27004298L)), .Names = c("R2", > "position")))), class = "igraph") > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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