Re: [igraph] plot.igraph and x-axis

[Gábor Csárdi]

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 <address@hidden> 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)$y))
> axis (1)
> axis (2) #result: plot 2
>
> Actually I want the graphic of plot 2 and the x-axis of plot 1.
>
> dput (gs)
> structure(list(5, FALSE, c(1, 2, 3, 4, 2, 3, 4, 3, 4, 4), c(0,
> 0, 0, 0, 1, 1, 1, 2, 2, 3), c(0, 1, 4, 2, 5, 7, 3, 6, 8, 9),
>     c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9), c(0, 0, 1, 3, 6, 10), c(0,
>     4, 7, 9, 10, 10), list(c(1, 0, 1), structure(list(), .Names =
> character(0)),
>         structure(list(name = c("rs59433790", "rs79037", "rs17343978",
>         "rs67257945", "rs55903329"), x = c(27428860L, 27433179L,
>         27433885L, 27434791L, 27436699L), y = c(0.8205112299125,
>         0.9363622429465, 0.93638580294825, 0.94247291459475,
>         0.78999608053825)), .Names = c("name", "x", "y")), structure(list(
>             weight = c(0.911066, 0.911768, 0.919415, 0.827461,
>             0.983026, 0.991462, 0.892149, 0.991467, 0.891518,
>             0.899993), y = c(0.925873823199, 0.787782242488667,
>             0.927452731221353, 0.894941333333333, 0.632980042374762,
>             0.634975016479238, 0.768939143570769, 0.883051666666667,
>             0.747102777275171, 0.995810294117647), color = c("red",
>             "red", "red", "red", "red", "red", "red", "red",
>             "red", "red")), .Names = c("weight", "y", "color"
>
>         )))), class = "igraph")
>
> Thanks
> Hermann
>
>
>
> 2013/11/26 Gábor Csárdi <address@hidden>
>>
>> On Tue, Nov 26, 2013 at 10:26 AM, Hermann Norpois <address@hidden>
>> wrote:
>> > I am sorry I did not get it.
>> > If I use rescale=FALSE my plot is empty.
>>
>> You also need to set the xlim and ylim parameters, because that also
>> defaults to (-1,1).
>>
>> > Actually I would like to change the rescale parameters. Is that
>> > possible,
>> > i.e.
>> > rescaleparameters = V(gs)$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)$y))
>> >>
>> >
>> >
>> > 2013/11/26 Gábor Csárdi <address@hidden>
>> >>
>> >> Hi,
>> >>
>> >> no, this is an igraph thing, igraph rescales layouts to (-1, 1),
>> >> unless you specify the rescale=FALSE:
>> >>
>> >> http://igraph.sourceforge.net/doc/R/plot.common.html
>> >>
>> >> Gabor
>> >>
>> >> On Tue, Nov 26, 2013 at 9:53 AM, Hermann Norpois <address@hidden>
>> >> wrote:
>> >> > Hello,
>> >> >
>> >> > I want to have an x-axis with x-values refering to V(g)$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
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>> >> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >> >
>> >>
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