[prev in list] [next in list] [prev in thread] [next in thread] 

List:       bioc-devel
Subject:    Re: [Bioc-devel] small request on graph::graphBAM()
From:       Robert Castelo <robert.castelo () upf ! edu>
Date:       2013-02-19 22:20:36
Message-ID: 5123FAB4.9060004 () upf ! edu
[Download RAW message or body]

hi Valerie,

thanks a lot for implementing this!!

regarding addNode() i have no specific request or opinion about it.


best regards,
robert.


On 2/19/13 9:44 PM, Valerie Obenchain wrote:
> This change is now implemented in devel 1.37.6.
> 
> > nms <- paste0("Y", 8:11)
> > df <- data.frame(from=nms, to=nms, weight=rep(1, 4))
> 
> Node names are not sorted when full vector of names is provided:
> > nodes(graphBAM(df, nodes=c(nms, "foo")))
> [1] "Y8"  "Y9"  "Y10" "Y11" "foo"
> 
> Names are sorted when only a zero-degree node is provided:
> > nodes(graphBAM(df, nodes="foo"))
> [1] "foo" "Y10" "Y11" "Y8"  "Y9"
> 
> 
> A side effect of this change is that addNode(), which calls 
> graphBAM(), was returning unsorted node names. To remain consistent 
> with previous behavior I've sorted these results. Currently addNode() 
> has no way to specify a full list of node names. Do you have an 
> opinion on addNode() behavior? OK as is?
> 
> 
> 
> Valerie
> 
> 
> 
> 
> On 02/07/2013 08:52 AM, Robert Castelo wrote:
> > Great, thanks!
> > robert.
> > 
> > On 02/07/2013 05:44 PM, Valerie Obenchain wrote:
> > > Hi Robert,
> > > 
> > > I will look into this next week. Thanks for providing details and
> > > examples in the request.
> > > 
> > > Valerie
> > > 
> > > On 02/06/2013 04:10 PM, Robert Castelo wrote:
> > > > dear maintainers of the graph package,
> > > > 
> > > > i have a small request for the constructor function graphBAM() from 
> > > > the
> > > > graph package.
> > > > 
> > > > the current help page of the graphBAM() constructor says the following
> > > > about the argument called 'nodes':
> > > > 
> > > > A character vector of node labels. Use this to add degree
> > > > zero nodes to the graph. If ‘NULL’, the set of nodes found
> > > > in ‘from’ and ‘to’ will be used.
> > > > 
> > > > It would be great if when nodes != NULL and includes the set of nodes
> > > > found in 'from' and 'to', 'nodes' would be taken as the set of 
> > > > nodes of
> > > > the graph, without re-ordering it.
> > > > 
> > > > currently this function has the following line (*):
> > > > 
> > > > nodes <- sort(unique(c(as.character(df$from), as.character(df$to),
> > > > nodes)))
> > > > 
> > > > this is a bit of a headache for me because the alphabetical 
> > > > ordering of
> > > > vertices does not respect integer ordering (obviously):
> > > > 
> > > > library(graph)
> > > > df <- data.frame(from=paste0("Y", 1:10), to=paste0("Y", 2:11),
> > > > weight=rep(1, 10))
> > > > nodes(graphBAM(df, nodes=paste0("Y", 1:10)))
> > > > [1] "Y1" "Y10" "Y11" "Y2" "Y3" "Y4" "Y5" "Y6" "Y7" "Y8" "Y9"
> > > > 
> > > > however, because i often deal with vectors of vertex labels created as
> > > > 
> > > > v <- paste0("Y", 1:p)
> > > > 
> > > > with p whatever positive integer, my vector of vertex labels is not
> > > > identical to the vector returned by graph::nodes() which 
> > > > complicates the
> > > > way i have to deal with this feature. re-ordering my vector of vertex
> > > > labels by alphabetical order implies doing it *each* time i do one of
> > > > those 'paste0()' calls, which is quite often, and this seems quite
> > > > common, see
> > > > http://simplystatistics.org/2013/01/31/paste0-is-statistical-computings-most-influential-contribution-of-the-21st-century \
> > > >  
> > > > 
> > > > 
> > > > > )
> > > > 
> > > > for this reason it would be great for me if the argument 'nodes' in
> > > > graphBAM() would have this additional functionality of forcing an
> > > > ordering on the vertex labels when 'nodes' include all vertices 
> > > > forming
> > > > the given edges.
> > > > 
> > > > i think this would amount to replacing the line above (*) by
> > > > 
> > > > stopifnot(all(!duplicated(nodes))) ## given nodes should be unique
> > > > edgeNodes <- unique(c(as.character(df$from), as.character(df$to))
> > > > if (!all(edgeNodes %in% nodes))
> > > > nodes <- sort(unique(c(nodesEdges, nodes)))
> > > > 
> > > > note that with this code when one just adds extra degree zero 
> > > > nodes, the
> > > > behavior does not change with respect to what it is doing right now 
> > > > and
> > > > if one likes to stick to the alphabetical ordering, you can always 
> > > > give
> > > > 'nodes=sort(myvertexlabels)' as argument to the graphBAM() constructor
> > > > function.
> > > > 
> > > > thanks!!
> > > > robert.
> > > > 
> > > > _______________________________________________
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > > 
> > 
> 

_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


[prev in list] [next in list] [prev in thread] [next in thread]