Error on first example in the tutorial

[chrismlarson]

I'm trying to follow the examples here: https://briatte.github.io/ggnet/

And I'm getting this error:

Error: Each variable must be a 1d atomic vector or list.
Problem variables: 'x', 'y', 'xend', 'yend'

Is there something wrong with my environment? I tried starting clean, but I'm rather new to R.

The code I'm using:

> library(GGally)
> library(network)
> library(sna)
> library(ggplot2)
>
> # random graph
> net = rgraph(10, mode = "graph", tprob = 0.5)
> net = network(net, directed = FALSE)
> 
> # vertex names
> network.vertex.names(net) = letters[1:10]
> 
> ggnet2(net)
Loading required package: scales
Error: Each variable must be a 1d atomic vector or list.
Problem variables: 'x', 'y', 'xend', 'yend'

[tbrambor]

I am having the same issue. This also extends to the use of ggnetwork() to fortify a network map for ggplot2.

Others seem to be experiencing the error as well. Here is a related stackoverflow question.

Any suggestions on how to correct this?

[subinoy]

I am having the same issue.

ggnet2(net2, node.size=6, node.color="black", edge.size=1, edge.color="grey") Error: Each variable must be a 1d atomic vector or list. Problem variables: 'x', 'y', 'xend', 'yend'

[aleferna]

same here

[subinoy]

Hi Francois, would you comment on this issue. It seems everyone having the same problem. Please look at this and suggest a solution. Thanks!!

[kbrevs]

Also getting the same issue - anyone stumble on a solution? Thanks!

[chrismlarson]

I'm on a fresh machine and I'm not seeing this anymore. But I think playing around with the order you load the libraries may help... There's got to be a conflict in there somewhere.

> library(GGally)
> library(network)
> library(sna)
> library(ggplot2)

[mevers]

Hi Francois.

Would you be able to provide an update on this issue? The problem still persists.

set.seed(2017);
net <- network(rgraph(20, mode = "graph", tprob = 0.5), directed = FALSE);
network.vertex.names(net) = letters[1:10];
ggnet2(net);
Error: Columns `x`, `y`, `xend`, `yend` must be 1d atomic vectors or lists

Unfortunately this seems to completely break ggnet2.

For what it's worth, here's my sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] scales_0.5.0.9000    ggplot2_2.2.1.9000   sna_2.4
[4] statnet.common_4.0.0 network_1.13.0       GGally_1.3.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13       reshape_0.8.7      grid_3.4.0         plyr_1.8.4
 [5] gtable_0.2.0       rlang_0.1.2        lazyeval_0.2.1     RColorBrewer_1.1-2
 [9] tools_3.4.0        munsell_0.4.3      compiler_3.4.0     colorspace_1.3-2
[13] tibble_1.3.4

[SJohnsonMayo]

I was able to use this package succesfully until this week when this error started appearing -- has anyone figured out how to deal with it?

[malcolmbarrett]

For some reason, x, y, xend, and yend are matrices. (using a ggnetwork-ified df) I dealt with it like this: df_net %>% purrr::map_df(~if (is.matrix(.x)) as.double(.x) else .x)

[zslehoczky]

I think I've found a solution for the issue, at least on my machine. I'm running R 3.4.3 on Win 10, but this is probably not platform-related.

Until now I've had the CRAN version of GGally installed, along with network and sna, just as mentioned in the example, and this setup threw the exact same error that a lot of people mentioned above. I was confused as the original network object doesn't even have members like x, xend, etc. It turned out that these are in fact members of the ggnetwork object, which is created invisibly during the command ggnet(). (ggnetwork vignette).

So I've tried installing ggnetwork: install.packages("ggnetwork") along with the source version of ggnet (devtools::install_github("briatte/ggnet")).

• ggnetwork was installed succesfully, but the package couldn't be loaded because it said that ggplot2 is not installed (which I've found strange because it's a package that I use on a daily basis as part of the tidyverse library).

• ggnet installation failed for some reason related to packages being already loaded.

I've restarted the R session, tried loading ggnetwork again, which again failed for lack of ggplot2, so I installed ggplot2. I tried once again installing ggnet from source, (this time before any packages were loaded) and it worked.

So, to sum it up: After restarting the R session:

install.packages("ggnetwork")
install.packages("ggplot2")
devtools::install_github("briatte/ggnet")

I don't know exactly which step did it, but afterwards the example script produced a graph plot, just as it was supposed to:

library(ggnetwork)
library(network)
library(sna)
library(ggnet)

net = rgraph(10, mode = "graph", tprob = 0.5)
net = network(net, directed = FALSE)

network.vertex.names(net) = letters[1:10]

ggnet2(net)

[KasperSkytte]

@zslehoczky Confirmed to work here aswell. So this seems to have something to do with the order by which packages are loaded and thus conflicting function names across namespaces. Always a good idea to specifically call functions from their correct packages by package::function...

[f0nzie]

Confirmed to work as well in vignette "examples-from-paper.Rmd" of package ggCompNet. After reinstalling as per @zslehoczky, the packages in this order:

## pre-load
library(ggnetwork)
library(network)
library(sna)
library(GGally)
library(geomnet)
library(igraph)

[briatte]

Dear all ~

Sorry for not answering this thread earlier.

As my StackOverflow answer says, the issue you were facing back then seems to be related either to what tibble accepts as a 'tidy' data frame. This would have affected 'tidyverse' packages as you reported back then.

The issue seems to be solved by now, given that I can run the code below (taken from the StackOverflow question mentioned above) either with or without the tidyverse loaded.

library(dplyr)
library(nycflights13)
library(igraph)
library(sna)
library(ggnetwork)

df_edges <- flights %>% group_by(origin, dest) %>% summarize(weight = n()) 
net <- graph.data.frame(df_edges, directed = T) 
V(net)$degree <- centralization.degree(net)$res 
df_net <- ggnetwork(net, layout = "fruchtermanreingold", weights = "weight", niter = 5000) 
ggplot(df_net, aes(x = x, y = y, xend = xend, yend = yend)) + 
  geom_edges(size = 0.4, alpha = 0.25) + 
  geom_nodes(aes(size = degree, text = vertex.names)) + 
  ggtitle("Network Graph of U.S. Flights Outbound from NYC in 2013") + 
  theme_blank()

In all cases, apologies again for leaving this issue unresolved by then, but I do remember that, after the ggplot2 v2.0.0 update and when the tidyverse arrived, things were very much in flux and breaking all around. Namespace conflicts are now better handled by R (and the tidyverse), so I hope that there won't be another of these threads in the future.

[briatte]

P.S. Since you're all here, let me advertise a bit.

To plot networks with R and ggplot2, try ggnetwork or, for even more flexibility (and probably more robust support of issues like the one in this thread), ggraph.