Entering edit mode
dear list, and particularly maintainers of the graph package,
i have encounter a problem with the graph package which i'll reproduce
using the example code from the help page of the graphBAM()
constructor
function:
example(graphBAM) ## run the entire example code, this creates a
data.frame called 'df'
df
from to weight
1 a b 2.3
2 a c 2.3
3 b c 4.3
4 c d 1.0
5 d a 3.0
## using the previous data frame, i'm going to re-run some of the
instructions of the example, starting by creating a fresh new graphBAM
object 'g'
g <- graphBAM(df)
g
A graphBAM graph with undirected edges
Number of Nodes = 4
Number of Edges = 5
## now i'm going to add a 'color' attribute to the nodes setting its
default value to 'green', this is taken again from the example
nodeDataDefaults(g, attr ="color") <- "green"
nodeData(g)
$color
$color$a
[1] "green"
$color$b
[1] "green"
$color$c
[1] "green"
$color$d
[1] "green"
## now i'm going to extract the subgraph induced by nodes 'a', 'c' and
'd' (taken again from the example)
sg <- subGraph(c("a","c","d"), g)
Error in nodeData(g, attr = att) : attribute not found: ?color?
## as you see i get an error related to the attribute previously
added.
however if, as it happens in the example, i change the value of the
'color' attribute to some of the nodes, the problem does not show up:
nodeData(g,n=c("b", "c"), attr ="color") <- "red"
nodeData(g, nodes(g))
$color
$color$a
[1] "green"
$color$b
[1] "red"
$color$c
[1] "red"
$color$d
[1] "green"
sg <- subGraph(c("a","c","d"), g)
sg
A graphBAM graph with undirected edges
Number of Nodes = 3
Number of Edges = 3
## the 'green' color in particular does not seem to be problem :)
nodeData(g,n=c("b", "c"), attr ="color") <- "green"
nodeData(g, nodes(g))
$color
$color$a
[1] "green"
$color$b
[1] "green"
$color$c
[1] "green"
$color$d
[1] "green"
sg <- subGraph(c("a","c","d"), g)
sg
A graphBAM graph with undirected edges
Number of Nodes = 3
Number of Edges = 3
i would expect/like that once an attribute has been added with its
value
by default, one can already apply the subGraph() function without
having
to update the attribute. could the package be fixed this way?
thanks!!
robert.
ps: sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.36.1 vimcom_0.9-5 setwidth_1.0-3 colorout_1.0-0
loaded via a namespace (and not attached):
[1] BiocGenerics_0.4.0 stats4_2.15.2 tools_2.15.2
