[BioC] graph::join discards node and edge attributes

[Paul Shannon]

Hi Nishant,

This is very good news -- I like your solution.

Could you venture out on a limb and predict when the new graph classes will be ready for testing?  They have features I'd like to use in the next (or some subsequent) version of RCytoscape.

 - Paul


On Dec 1, 2010, at 1:48 PM, Nishant Gopalakrishnan wrote:

> Hi Paul,
> 
> The join/union/ intersect methods for the graph objects do not preserve
> the edge or the node attributes. I do not think there are any plans to
> add this feature the old graph classes.
> 
> However, the new graphBAM class has methods that will hopefully do what
> you are looking for . The graphUnion method performs union of two graphs
> while preserving the node and edge attributes.  If there is a conflict
> of attributes, it is filled with NA. You do have the option of resolving
> the conflict by providing a named list of functions to the edgeFun or
> nodeFun arguments of the graphUnion method.
> The function should
>  1. take in two arguments and returns a conflict resolved value for the
> attribute.
>  2. have the same name as the attribute
> 
> I shall illustrate with some simple examples for the edge attributes below
> 
> ### Create two  graphs g1 and g2  with color and weight edge attributes
> from = c("a", "b", "d", "d")
> to   = c("b", "c", "y", "x")
> weight=c(1.2, 2.4, 5.4, 3.2)
> df <- data.frame(from, to, weight)
> g1 <- graphBAM(df, edgemode = "directed")
> edgeData(g1, attr = "color") <- "green"  ## set the default
> edgeData(g1, from = c("a","b"), to = c("b", "c") , attr = "color") <-
> c("yellow", "blue")
> 
> from = c("a", "b", "b", "d", "d")
> to   = c("b", "c", "d", "c", "x")
> weight=c(1.2, 4.2, 5.6, 2.1, 3.2)
> df <- data.frame(from, to, weight)
> g2 <- graphBAM(df, nodes = c("a","b","c", "d", "x", "y", "z"),
>    edgemode = "directed")
> edgeData(g2, attr = "color") <- "green"
> edgeData(g2, from =  c("a","b"), to = c("b", "c") , attr = "color") <-
> c("yellow", "cyan")
> 
> ## confilicting attributes are filled with NA in the result
> g <- graphUnion(g1, g2)  
> edgeData(g, attr = "weight")  
> edgeData(g, attr = "color")
> 
> ## Provide a function for resolving conflicting weight attribute, I want
> the sum of
> ## weights in case of conflict
> g <- graphUnion(g1, g2, edgeFun = list(weight = sum))
> edgeData(g, attr = "weight")
> edgeData(g, attr = "color")
> 
> If you wanted to resolve the conflict for the attribute color for the
> edges, you could write a function
> myFun <- function(x, y) {
>  ## resolve conflict here
> }
> and pass it  an argument to the graphUnion method.
> g <- graphUnion(g1, g2, edgeFun = list(weight = sum, color = myFun))
> 
> Node attributes if present are also handled in exactly the same manner.
> If conflicting node attributes occur in the union process , there is
> another argument  nodeFun that you can use to pass in a function for
> resolving the conflict.
> 
> I hope that answers your question.
> 
> Nishant
> 
> On 11/29/2010 09:11 AM, Paul Shannon wrote:
>> I have two well-annotated kegg pathway graphs I wish to merge.
>> 
>> Using graph::join, the nodes and edges merge nicely, but all the edge and node attributes are lost, and a new edge attribute 'weight' is added.
>> 
>> 
>>> names (nodeDataDefaults (g.05200))  
>>> 
>>   [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
>> 
>>> names (nodeDataDefaults (g.04010))  
>>> 
>>   [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
>> 
>>> names (nodeDataDefaults (g.both))   
>>> 
>>  NULL
>> 
>> 
>> 
>>> names (edgeDataDefaults (g.04010))
>>> 
>>  [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
>> 
>>> names (edgeDataDefaults (g.05200))
>>> 
>>  [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
>> 
>>> names (edgeDataDefaults (g.both))
>>> 
>>  [1] "weight"
>> 
>> Is there any graph method, current or planned, which will preserve node and edge attributes?  I realize that attribute conflicts can arise, and some strategy is required to handle these.
>> 
>> - Paul
>> 
>> 
>> 
>>> sessionInfo ()
>>> 
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] RCytoscape_1.1.6     org.Mm.eg.db_2.4.1   RCurl_1.4-3          bitops_1.0-4.1       GOstats_2.16.0       Category_2.16.0      GO.db_2.4.5
>> [8] GSEABase_1.11.2      annotate_1.28.0      KEGG.db_2.4.1        KEGGgraph_1.4.0      graph_1.26.0         XML_3.2-0            SPIA_1.8.0
>> [15] org.Hs.eg.db_2.4.6   RSQLite_0.9-2        DBI_0.2-5            AnnotationDbi_1.11.8 Biobase_2.10.0       RUnit_0.4.26
>> 
>> loaded via a namespace (and not attached):
>> [1] genefilter_1.32.0 RBGL_1.25.0       splines_2.12.0    survival_2.35-8   tools_2.12.0      XMLRPC_0.2-2      xtable_1.5-6
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>