Re: [igraph] igraph slow when plotting

[Gábor Csárdi]

On Fri, Feb 28, 2014 at 7:38 AM, Simone Gabbriellini <address@hidden> wrote:

Hi Gabor,

I see nodes are placed one by one, but without the shape modification this happens so quick I cannot even tell it’s happening, but if I modify the shape, then all is slowed down so that I can see each node when it’s plotted.

to be more precise:
- if all nodes have the same shape (circle, square, whatever), plotting is fast
- if nodes have different shapes (some circle, some square), then plotting is very slow

Yes, because they are plotted one by one by igraph, if there are different shapes. In base R graphics, there is no way to plot different vertex shapes in a single go. 

What we could do is plotting all square at once, and then all circles at once, etc. This is reasonable request:

https://github.com/igraph/igraph/issues/592

 

I am on Mac OSX 10.9.1 and run R version 3.0.2 and igraph 0.6.6

It is actually not igraph that is slow, but the quartz device of OSX. If you are using the x11() device, it is much faster, but of course it'll look worse, there is no anti-aliasing. Everything is smooth and fast on linux and windows.

Still, with many vertices, I think it is worth using the x11() device to experiment.

G.

 

here’s a sample data frame to use with my code (with more nodes, you will see more slowness ):

df<-structure(list(id = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12), name = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "l", "m", "n"), village = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "L", "M", "N"), religion = c("x", "y", "y", "y", "y", "x", "x", "x", "x", "x", "y","x"), adoption.lag = c(30, 32, 32, 32, 0, 30, 30, 30, 0, 1, 22, 22), type = c("potter", "potter", "potter", "potter", "city", "potter", "potter", "potter", "potter", "potter", "city", "potter")), .Names = c("id", "name", "village", "religion", "adoption.lag", "type"), row.names = c(NA, -12L), class = "data.frame”)

thanks,
Simone

Il giorno 28/feb/2014, alle ore 13:04, Gábor Csárdi <address@hidden> ha scritto:

> Hi Simone,
>
> > library(igraph)
> > g<-graph.empty(n=0, directed=T)
> > # add nodes
> > g<-add.vertices(g, length(df[,1]), attr=df)
> Error in add.vertices(g, length(df[, 1]), attr = df) :
>   please supply names for attributes
>
> please send reproducible code, and information about your platform.
>
> Vertices are indeed plotted one by one if they have different shapes.
>
> Gabor
>
>
> On Fri, Feb 28, 2014 at 6:29 AM, Simone Gabbriellini <address@hidden> wrote:
> Dear List,
>
> I have observed a strange behavior in igraph with R. If I do:
>
> g<-graph.empty(n=0, directed=T)
> # add nodes
> g<-add.vertices(g, length(df[,1]), attr=df)
> # plot
> plot(g, vertex.size=3, vertex.label.cex=0.7, vertex.label.dist=0.3)
>
> it’s fast as usual, but if I do:
>
> g<-graph.empty(n=0, directed=T)
> # add nodes
> g<-add.vertices(g, length(df[,1]), attr=df)
> # shape visualization, if type = city -> squared, else circle
> V(g)[type=="city"]$shape<-"square"
> V(g)[type=="potter"]$shape<-"circle"
> # plot
> plot(g, vertex.size=3, vertex.label.cex=0.7, vertex.label.dist=0.3)
>
> then it looks like it plots vertices one by one… and it takes considerably more time… any guess where I am wrong?
>
> best,
> Simone
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