Entering edit mode
hi,
the function edgeData() from the Bioconductor graph package seems to
have a problem with the way it stores and retrieves edge atributes.
After investigating the issue i think it has to do with setting and
retrieving edge attributes for a subset of the edges, as opposed to
doing it for all edges at once. here is a minimal example that
reproduces the problem:
library(graph)
df <- data.frame(from=c("a", "b", "c"),
to=c("b", "c", "d"),
weight=rep(1, 3), stringsAsFactors=FALSE)
g <- graphBAM(df)
## this builds the undirected graph a-b-c-d
## set a new edge attribute "a" with 0 by default
edgeDataDefaults(g, attr="a") <- 0
## set the "a" attribute of all edges to 1
edgeData(g, from=df$from, to=df$to, attr="a") <- 1
## show the value of the "a" attribute for all edges,
## everything works as expected
edgeData(g, from=df$from, to=df$to, attr="a")
$`a|b`
[1] 1
$`b|c`
[1] 1
$`c|d`
[1] 1
## now repeat the operation but setting the "a" attribute
## only for the first edge a-b
g <- graphBAM(df)
edgeDataDefaults(g, attr="a") <- 0
edgeData(g, from=df$from[1], to=df$to[1], attr="a") <- 1
edgeData(g, from=df$from, to=df$to, attr="a")
$`a|b`
[1] 0
$`b|c`
[1] 1
$`c|d`
[1] 0
as you see, the value 1 is not set for the first edge "a|b" but for
the
second "b|c". if i repeat the operation setting the edge attribute "a"
for the last two edges, it goes also wrong:
g <- graphBAM(df)
edgeDataDefaults(g, attr="a") <- 0
edgeData(g, from=df$from[2:3], to=df$to[2:3], attr="a") <- 1
edgeData(g, from=df$from, to=df$to, attr="a")
$`a|b`
[1] 1
$`b|c`
[1] 0
$`c|d`
[1] 1
since the attribute is set to edges "a|b" and "c|d" while it should
have
been set to "b|c" instead of "a|b".
i put my sessionInfo() below which correspond to the release version
of
the package but i can also reproduce it in the devel version.
thanks!
robert.
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.36.2 vimcom_0.9-7 setwidth_1.0-3 colorout_0.9-9
loaded via a namespace (and not attached):
[1] BiocGenerics_0.4.0 stats4_2.15.1 tools_2.15.1
