[BioC] Edge attributes in Rgraphviz

[Srinivas Iyyer]

Dear Prof. Gentleman, 

I was using 1.16 and updated it to 1.17 version of
Graphviz.  I see same problem with 1.17. am I wrong in
assigning attributes to edges?

 Here I do not intend to change some edges but all
edges in the entire graph. I feel that the lines are
too fat at some places in the graph. 

Kind regards, 
Srini.


> x = buildEdgeList(g4,
+                     recipEdges='distinct',
+                     edgeAttrs=list(c(color='green'))
+                    )
Error in buildEdgeList(g4, recipEdges = "distinct",
edgeAttrs = list(c(color = "green"))) : 
  STRING_ELT() can only be applied to a 'character
vector', not a 'NULL'


> natt = makeNodeAttrs(
+                       g4, 
+                       shape = "ellipse", 
+                       fillcolor= "goldenrod1",
+                       size=0,
+                       fontsize=8,
+                       label = substr(nodes(g4),6,
10)
+                      )

>  lgGO = agopen(
+               g4, 
+               recipEdges = "distinct", 
+               layoutType = "dot",
+               nodeAttrs = natt, 
+               name = "",
+               edgeAttrs=list(c(color='green',
+                                weight=0.3)
+                              )
+               )
Error in buildEdgeList(graph, recipEdges, edgeAttrs,
subGList, attrs$edge) : 
  STRING_ELT() can only be applied to a 'character
vector', not a 'NULL'



> sessionInfo()
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United
States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United
States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices
utils     datasets  methods   base     

other attached packages:
 [1] Rgraphviz_1.17.7    rgug4130a.db_2.0.2 
GOstats_2.4.0       Category_2.4.0     
genefilter_1.16.0   survival_2.34       RBGL_1.14.0   
    
 [8] annotate_1.16.1     xtable_1.5-2       
GO.db_2.0.2         AnnotationDbi_1.0.6 RSQLite_0.6-4 
     DBI_0.2-4           Biobase_1.16.2     
[15] graph_1.16.1       

loaded via a namespace (and not attached):
[1] cluster_1.11.9




--- Robert Gentleman <rgentlem at fhcrc.org> wrote:

> You did not tell us what version - please include
> the output of 
> sessionInfo in your posts.
> 
> Things have changed a lot and the devel version
> 1.17.11 is somewhat 
> improved. Is that what you are using, and if not
> could you please try it?
> 
> best wishes
>    Robert
> 
> 
> Srinivas Iyyer wrote:
> > Dear group, 
> > 
> > I am finding difficult to control edge size and
> color
> > in the following piece of code. 
> > natt = makeNodeAttrs(
> >                      g4, 
> >                      shape = "ellipse", 
> >                      fillcolor= "goldenrod1",
> >                      size=0,
> >                      fontsize=8,
> >                      label = substr(nodes(g4),6,
> 10)
> >                     )
> >> lgGO = agopen(
> >              g4, 
> >              recipEdges = "distinct", 
> >              layoutType = "dot",
> >              nodeAttrs = natt, 
> >              name = "",
> >              edgeAttrs=list(c(color='green',
> >                               weight=0.3)
> >                             )
> >              )
> > 
> > Error in buildEdgeList(graph, recipEdges,
> edgeAttrs,
> > subGList, attrs$edge) : 
> >   STRING_ELT() can only be applied to a 'character
> > vector', not a 'NULL'
> > 
> > 
> > Here in agopen, I made a edgeAttrs list object
> with 
> > color and weight attributes and I get above error.
> 
> > 
> > 
> > Instead, I tried like the following:
> > 
> >> x = buildEdgeList(g4,
> >                     recipEdges='distinct',
> >                    
> edgeAttrs=list(c(color='green'))
> >                    )
> > Error in buildEdgeList(g4, recipEdges =
> "distinct",
> > edgeAttrs = list(c(color = "green"))) : 
> >   STRING_ELT() can only be applied to a 'character
> > vector', not a 'NULL'
> > 
> > 
> > Also when I just make a buildEdgeList object, I
> can
> > make it with wight=1 (which is default)
> > 
> > 
> > 
> >> x = buildEdgeList(g4,recipEdges='distinct')
> >> y = unlist(x)
> >> y[[1]]
> > An object of class “pEdge”
> > Slot "from":
> > [1] "GO:0030199"
> > 
> > Slot "to":
> > [1] "GO:0030198"
> > 
> > Slot "attrs":
> > $arrowhead
> > [1] "open"
> > 
> > $weight
> > [1] "1"
> > 
> > $dir
> > [1] "forward"
> > 
> > 
> > Slot "subG":
> > [1] 0
> > 
> > 
> > 
> > How can I control, the edge global parameters. 
> > I do not see makeEdgeAttr function just like
> > makeNodeAttr. Could some one help me here please.
> A
> > working code is given at bottom. 
> > 
> >> makeEdgeAttrs
> > Error: object "makeEdgeAttrs" not found
> > 
> > 
> > 
> > 
> > 
> > ##### code that works#######
> > g4 <- GOGraph(summary(hgOver)$GOBPID, GOBPPARENTS)
> > 
> > natt = makeNodeAttrs(g4, shape = "ellipse",
> fillcolor
> > = "goldenrod1",size=0,fontsize=8,label =
> > substr(nodes(g4),6, 10))
> > 
> > natt$fillcolor[summary(hgOver)$GOBPID] = "red" 
> > 
> > lgGO = agopen(g4, recipEdges = "distinct",
> layoutType
> > = "dot",nodeAttrs = natt, name =
> > "",edgeAttrs=list(c(color='green')))
> > 
> > plot(lgGO)
> > 
> > ###### end of code that works #######
> > 
> > 
> >      
>
____________________________________________________________________________________
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> > 
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> > 
> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
> 
> 



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