[BioC] bug in graph::edgeData()

[Robert Castelo]

Dear Paul,

coming back to your temporary solution to this bug, please see below ...

On 02/16/2013 01:31 AM, Paul Shannon wrote:
> Hi Robert,
>
> Thanks for the bug report.  I reproduced the problem and made some progress -- but not enough -- in unraveling the faulty logic which causes it.  I offer here a workaround which might help you proceed with your work while I continue to work on the bug.
>
> The workaround depends upon converting your graphBAM to a graphAM, as demonstrated below.  If your graph is very large, this may not be practical.
>
> In the code below, I reproduce the error, convert the graphBAM to a graphAM, then get the right result.
>
> I will continue working on the bug.  Let us know if this workaround is helpful.
>
>   - Paul
>
>
>
> library(graph)
> df<- data.frame(from=c("a", "b", "c"),
>                   to=c("b", "c", "d"),
>                   weight=rep(1, 3), stringsAsFactors=FALSE)
> g.orig<- graphBAM(df)
> g<- g.orig
> edgeDataDefaults(g, attr="a")<- 0
> edgeData(g, from="a", to="b", attr="a")<- 1
> edgeData(g, attr="a", from="a")
>    # $`a|b`
>    # [1] 1
>
> edgeData(g, attr="a", from="a", to="b")  # bug
>    # $`a|b`
>    # [1] 0
>
>
> g<- as(g.orig, "graphAM")
> edgeDataDefaults(g, attr="a")<- 0
> edgeData(g, from="a", to="b", attr="a")<- 1
> edgeData(g, attr="a", from="a")
>    # $`a|b`
>    # [1] 1
>
> edgeData(g, attr="a", from="a", to="b")  # no bug
>    # $`a|b`
>    # [1] 1

to facilitate using this workaround in my code, it would be useful for 
me to be able to coerce the graphAM object back to a gaphBAM object with 
all attributes, however it seems that this coercion is not copying the 
attributes:

gbam <- as(g, "graphBAM")
gbam
A graphBAM graph with undirected edges
Number of Nodes = 4
Number of Edges = 3
edgeData(gbam, attr="a", from="a", to="b")  # no bug
Error in .verifyBAMAttrs(self, attr) : 'attr' not found: ‘a’


could you fix the coercion from graphAM to graphBAM such that all 
attributes from the graphAM object are copied into the graphBAM object?

thanks!!
robert.
ps: sessionInfo()

R Under development (unstable) (2012-10-07 r60893)
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_1.37.6   vimcom_0.9-7   setwidth_1.0-3 colorout_1.0-0

loaded via a namespace (and not attached):
[1] BiocGenerics_0.5.6 parallel_2.16.0    stats4_2.16.0 
tools_2.16.0


>
> On Feb 15, 2013, at 2:49 AM, Robert Castelo wrote:
>
>> 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
>>
>> _______________________________________________
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>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550