Hi Yannick,
On Mon, Mar 11, 2013 at 7:28 AM, Yannick Rochat <[email protected]>wrote:
> Dear all,
>
>
> I have lists in which elements are graphs, like :
>
> graphs <- lapply(c(100,1000), graph.atlas)
>
>
> In order to plot them, I would like to compute sizes of vertices depending
> on degree, color, labels, etc. Idem with edges and layouts. I have found a
> way to do that with the apply family, but it is not elegant and I'm not
> confident about it :
>
> graphs <- lapply(graphs, function(x) {V(x)$size <- degree(x) ; x})
>
This is about the best you can do here. You cannot simply do
graphs <- lapply(graphs, function(x) { V(x)$size <- degree(x) })
because then your anonymous function returns V(x)$size and that is put into
'graphs'. This is not specific to igraph, all replacement functions are
like that IMHO:
v <- 1:5
x <- length(v) <- 10
v
# [1] 1 2 3 4 5 NA NA NA NA NA
x
# [1] 10
Finally, I've decided to use 'for', but found myself with a problem I don't
> understand. Why this
>
> for (i in 1:length(graphs)) V(graphs[[i]])$size <- degree(graphs[[i]])
>
> works is clear to me, but why that
>
> for (g in graphs) V(g)$size <- degree(g)
>
> doesn't isn't (in print(graphs) the size attribute is missing).
>
It seems that R copies graphs, and you are working on the copy in the loop,
and the original objects are unaffected. Again, this is not specific to
igraph, it is an R thing:
vectors <- list(1:5, 1:10)
for (v in vectors) length(v) <- 20
vectors
# [[1]]
# [1] 1 2 3 4 5
#
# [[2]]
# [1] 1 2 3 4 5 6 7 8 9 10
for (i in 1:length(vectors)) length(vectors[[i]]) <- 20
vectors
# [[1]]
# [1] 1 2 3 4 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#
# [[2]]
# [1] 1 2 3 4 5 6 7 8 9 10 NA NA NA NA NA NA NA NA NA NA
[...]
my config :
> igraph 0.6-3
> R 2.15.1
>
Btw. consider upgrading to version 0.6.5, because we fixed many bugs and as
the release notes say:
"Many basic graph operations (eg. printing the summary to the screen,
querying attribute values) now avoid copying the graph, so these operations
are now much faster in R."
Best,
Gabor
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