|
| From: | Hermann Norpois |
| Subject: | Re: [igraph] plot.igraph and x-axis |
| Date: | Thu, 28 Nov 2013 16:54:02 +0100 |
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:
layout=cbind (V(gs)$x, V(gs)$y), 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,
G.
On Wed, Nov 27, 2013 at 6:26 PM, Gábor Csárdi <address@hidden> 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)$y), add=TRUE)
>
> G.
>
> On Wed, Nov 27, 2013 at 11:43 AM, Hermann Norpois <address@hidden> wrote:
>> Thanks for your answer.
>>
>> I tried and solved some problems. But there are new problems. There is a
>> suboptimal resolution in the y-dimension. And I cannot change the y-scale by
>> ylim:
>>
>> plot (gs, vertex.size=2, vertex.label=NA, rescale=FALSE, xlim=range
>> (V(gs)$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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>>> >
>>> >
>>> >
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>>
>>
>>
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