[BioC] graph::subGraph() problem with node attributes

[Valerie Obenchain]

Hi Robert,

Thanks for the bug report. This is now fixed in release 1.36.2 and devel 
1.37.5. Both should be available via biocLite() Tuesday after 9am PST.

Valerie



On 02/01/2013 02:50 PM, Robert Castelo wrote:
> 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
>
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