Great. Thank you.
2013/11/28 Gábor Csárdi <[email protected]> > So just for the record, this is not a bug, but in R default is to have > a 1:1 y/x aspect ratio. If you don't want to set an aspect ratio, you > can supply asp=0: > > plot (gs, vertex.size=2, vertex.label=NA, rescale=FALSE, > xlim=range (V(gs)$x), ylim= range (0,1), edge.width= > (E(gs)$weight)^6, > layout=cbind (V(gs)$x, V(gs)$y), asp=0) > > G. > > On Wed, Nov 27, 2013 at 6:26 PM, Gábor Csárdi <[email protected]> > wrote: > > Seems like a bug in igraph, although I have no time now to check. > > Here is a workaround: > > > > plot(NA, type="n", xlim=range(V(gs)$x), ylim=c(0,1), axes=FALSE, > > xlab="", ylab="") > > plot (gs, vertex.size=2, vertex.label=NA, rescale=FALSE, xlim=range > > (V(gs)$x), ylim=c(0,1), edge.width= (E(gs)$weight)^6, layout= cbind > > (V(gs)$x, V(gs)$y), add=TRUE) > > > > G. > > > > On Wed, Nov 27, 2013 at 11:43 AM, Hermann Norpois <[email protected]> > wrote: > >> Thanks for your answer. > >> > >> I tried and solved some problems. But there are new problems. There is a > >> suboptimal resolution in the y-dimension. And I cannot change the > y-scale by > >> ylim: > >> > >> plot (gs, vertex.size=2, vertex.label=NA, rescale=FALSE, xlim=range > >> (V(gs)$x), ylim= range (0,1), edge.width= (E(gs)$weight)^6, layout= > cbind > >> (V(gs)$x, V(gs)$y)) > >> axis (1) > >> axis (2) #result: plot 1 > >> > >> > >> plot (gs, vertex.size=2, vertex.label=NA, edge.width= (E(gs)$weight)^6, > >> layout= cbind (V(gs)$x, V(gs)$y)) > >> axis (1) > >> axis (2) #result: plot 2 > >> > >> Actually I want the graphic of plot 2 and the x-axis of plot 1. > >> > >> dput (gs) > >> structure(list(5, FALSE, c(1, 2, 3, 4, 2, 3, 4, 3, 4, 4), c(0, > >> 0, 0, 0, 1, 1, 1, 2, 2, 3), c(0, 1, 4, 2, 5, 7, 3, 6, 8, 9), > >> c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9), c(0, 0, 1, 3, 6, 10), c(0, > >> 4, 7, 9, 10, 10), list(c(1, 0, 1), structure(list(), .Names = > >> character(0)), > >> structure(list(name = c("rs59433790", "rs79037", "rs17343978", > >> "rs67257945", "rs55903329"), x = c(27428860L, 27433179L, > >> 27433885L, 27434791L, 27436699L), y = c(0.8205112299125, > >> 0.9363622429465, 0.93638580294825, 0.94247291459475, > >> 0.78999608053825)), .Names = c("name", "x", "y")), > structure(list( > >> weight = c(0.911066, 0.911768, 0.919415, 0.827461, > >> 0.983026, 0.991462, 0.892149, 0.991467, 0.891518, > >> 0.899993), y = c(0.925873823199, 0.787782242488667, > >> 0.927452731221353, 0.894941333333333, 0.632980042374762, > >> 0.634975016479238, 0.768939143570769, 0.883051666666667, > >> 0.747102777275171, 0.995810294117647), color = c("red", > >> "red", "red", "red", "red", "red", "red", "red", > >> "red", "red")), .Names = c("weight", "y", "color" > >> > >> )))), class = "igraph") > >> > >> Thanks > >> Hermann > >> > >> > >> > >> 2013/11/26 Gábor Csárdi <[email protected]> > >>> > >>> On Tue, Nov 26, 2013 at 10:26 AM, Hermann Norpois <[email protected]> > >>> wrote: > >>> > I am sorry I did not get it. > >>> > If I use rescale=FALSE my plot is empty. > >>> > >>> You also need to set the xlim and ylim parameters, because that also > >>> defaults to (-1,1). > >>> > >>> > Actually I would like to change the rescale parameters. Is that > >>> > possible, > >>> > i.e. > >>> > rescaleparameters = V(gs)$x > >>> > >>> No, that's not possible. Rescale the layout for yourself, and then set > >>> these limits in xlim and ylim. > >>> > >>> Btw. if you include code this way, that is somewhat a pain to try, > >>> because the > prompt makes it impossible to copy and paste. It is best > >>> to include some code that we can just copy and paste into R, without > >>> needing to edit it in emacs. > >>> > >>> G. > >>> > >>> > My try: > >>> > plot (gs, vertex.size=2, vertex.label=NA,rescale=FALSE, edge.width= > >>> > (E(gs)$weight)^6, layout=cbind (V(gs)$x, V(gs)$y)) > >>> > > >>> >> dput (gs) > >>> > structure(list(2, FALSE, 1, 0, 0, 0, c(0, 0, 1), c(0, 1, 1), > >>> > list(c(1, 0, 1), structure(list(), .Names = character(0)), > >>> > structure(list(name = c("rs744016", "rs763273"), x = > >>> > c(27042106L, > >>> > 27043594L), y = c(0.6445235948615, 0.6229189950958)), .Names > = > >>> > c("name", > >>> > "x", "y")), structure(list(weight = 0.986597, y = 0.7704755, > >>> > color = "red"), .Names = c("weight", "y", "color" > >>> > )))), class = "igraph") > >>> >> class (gs) > >>> > [1] "igraph" > >>> >> plot (gs, vertex.size=2, vertex.label=NA,rescale=FALSE, edge.width= > >>> >> (E(gs)$weight)^6, layout=cbind (V(gs)$x, V(gs)$y)) > >>> >> axis (1, at=1:10) # Does not change anything. > >>> >> plot (gs, vertex.size=2, vertex.label=NA, edge.width= > >>> >> (E(gs)$weight)^6, > >>> >> layout=cbind (V(gs)$x, V(gs)$y)) > >>> >> > >>> > > >>> > > >>> > 2013/11/26 Gábor Csárdi <[email protected]> > >>> >> > >>> >> Hi, > >>> >> > >>> >> no, this is an igraph thing, igraph rescales layouts to (-1, 1), > >>> >> unless you specify the rescale=FALSE: > >>> >> > >>> >> http://igraph.sourceforge.net/doc/R/plot.common.html > >>> >> > >>> >> Gabor > >>> >> > >>> >> On Tue, Nov 26, 2013 at 9:53 AM, Hermann Norpois < > [email protected]> > >>> >> wrote: > >>> >> > Hello, > >>> >> > > >>> >> > I want to have an x-axis with x-values refering to V(g)$x. > >>> >> > > >>> >> > How does this work? > >>> >> > > >>> >> > I tried > >>> >> > axis (1, at=V(g)$x) without an effect. > >>> >> > > >>> >> > dput (axis (1)) has the following output: > >>> >> > c(-1, -0.5, 0, 0.5, 1) > >>> >> > > >>> >> > How can I change this? I guess it is more a classical R-question > ... > >>> >> > > >>> >> > thanks > >>> >> > Hermann > >>> >> > > >>> >> > > >>> >> > _______________________________________________ > >>> >> > 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 > >>> > > >>> > > >>> > > >>> > _______________________________________________ > >>> > 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 > >> > >> > >> > >> _______________________________________________ > >> 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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