Entering edit mode
hi,
i have found a problem when using the functions addNode() and
edgeData()
from the graph package, which i believe is a bug and it can be
reproduced with the following minimal example:
library(graph)
## build a graphBAM object with vertices a, b, d, e and edges a-d, b-e
df <- data.frame(from=c("a", "b"),
to =c("d", "e"),
weight=rep(1, 2))
g <- graphBAM(df)
nodes(g)
[1] "a" "b" "d" "e"
## add a numerical attribute to one of the edges
edgeDataDefaults(g, "x") <- NA_real_
edgeData(g, from="a", to="d", "x") <- 1
unlist(edgeData(g, attr="x"))
a|d b|e d|a e|b
1 NA 1 NA
## add an extra node f to the graphBAM object and fetch edge
attributes
gOK <- addNode("f", g)
nodes(gOK)
[1] "a" "b" "d" "e" "f"
unlist(edgeData(gOK, attr="x"))
a|d b|e d|a e|b
1 NA 1 NA
## now comes the bug ...
## add an extra node c to the graphBAM object and fetch edge
attributes
gBUG <- addNode("c", g)
nodes(gBUG)
[1] "a" "b" "c" "d" "e"
unlist(edgeData(gBUG, attr="x"))
Error in data.frame(ft, tmp, stringsAsFactors = FALSE) :
arguments imply differing number of rows: 4, 6
traceback()
7: stop(gettextf("arguments imply differing number of rows: %s",
paste(unique(nrows), collapse = ", ")), domain = NA)
6: data.frame(ft, tmp, stringsAsFactors = FALSE)
5: .eAttrsFun(self, from = names(edges(self)), attr = attr)
4: as.list(.eAttrsFun(self, from = names(edges(self)), attr = attr))
3: edgeData(gBUG, attr = "x")
2: edgeData(gBUG, attr = "x")
1: unlist(edgeData(gBUG, attr = "x"))
from this output, my guess is that the problem is related to the first
line of code of the addNode() method in the R/methods-graphBAM.R file:
setMethod("addNode",
signature(node="character", object="graphBAM",
edges="missing"),
function(node, object) {
nds <- sort(unique(c(nodes(object), node)))
[...]
because if i simply remove the call to the function sort, i.e.,
replacing this line by
nds <- unique(c(nodes(object), node))
then the problem is solved. however, i don't know whether this has
other
consequences related to the design of the package. upfront, i do not
see
a reason why, internally to the package, vertices should be
alphabetically ordered.
best regards,
robert.
ps: sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.40.0 vimcom_0.9-91 setwidth_1.0-3 colorout_1.0-1
loaded via a namespace (and not attached):
[1] BiocGenerics_0.8.0 parallel_3.0.2 stats4_3.0.2
tools_3.0.2
