User: Paul Shannon

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Paul Shannon1.1k
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Posts by Paul Shannon

<prev • 107 results • page 1 of 11 • next >
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RCytoscape error with deleteSelectedEdges
... Hi Fahim, (I am redirecting the CC to the bioc mailing list, rather than bioc- devel, since that is the more appropriate venue for your question.) I think you have run into version confusion -- something that gets us all sooner or later. If you take these steps, I can pretty nearly guarantee ever ...
rcytoscape written 6.6 years ago by Paul Shannon1.1k
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graph classes: how to combine multiple graphs into a single graph
... Hi Nishant, After too long a delay, I am getting back to you on this. I apologize for that delay and also for this: as you point out, and as I sheepishly realize, I HAD asked this question before, and you had answered it. My confusion persists, however, in this form: it appears that the graphBA ...
graph written 6.7 years ago by Paul Shannon1.1k
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Comment: C: [R] RCytoscape setPosition error
... Hi Fahim, On Feb 20, Fahim M wrote: > Is there any function to find maxx, maxy, minx and miny? (x and y coordinate of the four corners of the Cy screen) This would be very useful -- I have wanted this myself. I will pass the request along to Jan Bot, the ever-helpful and resourceful developer ...
written 6.7 years ago by Paul Shannon1.1k
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Comment: C: [R] RCytoscape setPosition error
... Hi Fahim, I reworked your second (and failing) example so that it works. I will paste the code in below, along with a tiny example data file, so you can see the kind of nodes and edges I was testing with. Please keep this general scheme in mind. RCytoscape expects to be used primarily like this ...
written 6.7 years ago by Paul Shannon1.1k
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[R] RCytoscape setPosition error
... Hi Fahim, There is an easily resolved omission in the sample code you sent. Please note the the 3rd line below, 'displayGraph', which does not appear in your email. This method transmits your graph from R to Cytoscape, creating a Cytoscape network. cw <- CytoscapeWindow ('smallExample', gra ...
network cancer graph written 6.8 years ago by Paul Shannon1.1k • updated 6.8 years ago by Fahim Md250
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graph classes: how to combine multiple graphs into a single graph
... help (package='graph') describes many methods, but none of those mentioned seem to combine two graphs into a third -- perhaps even combining attributes along the way. graph::union looked promising, but is defined such that it only works if the nodes in each graph are identical. Any suggestions? ...
graph written 6.8 years ago by Paul Shannon1.1k • updated 6.8 years ago by Nishant Gopalakrishnan340
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Comment: C: difficulty loading rsbml
... Thanks for your replies, Dan and Martin. My original post mostly concealed that I do have libsbml installed. A quick test from python shows that it works: python can read the latest, full yeastNet sbml file. So the problem appears to be that something I have done, or not done, leads to rsbml not ...
written 6.8 years ago by Paul Shannon1.1k
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difficulty loading rsbml
... The specific error is see (text below) suggests that libsbml is not being found. ASTNode appears to be a symbol in libsbml biocLite ('rbsml') installing /usr/local/lib/libsbml.4.2.0.dylib export DYLD_LIBRARY_PATH=/usr/local/lib R > library (rsbml) I get this error message: Error : . ...
rsbml written 6.8 years ago by Paul Shannon1.1k • updated 19 months ago by den.kazakiewicz0
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names of edges in graph classes
... I notice that edges appear to be named in two different ways: > edgeNames (g) [1:2] [1] "1~2" "1~3" > names (edgeData (g)) [1:2] [1] "1|2" "1|3" Does this different choice for separator character -- tilde in one case, vertical bar in the other -- convey some meaning it would behoove me to ...
written 6.9 years ago by Paul Shannon1.1k • updated 6.9 years ago by Nishant Gopalakrishnan340
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Answer: A: Rgraphviz running problem on vista
... For some, RCytoscape might provide an alternative to Rgraphviz. It uses a Cytoscape plugin (which can be installed from within either Cytoscape 2.7 or 2.8) and Duncan Temple Lang's XMLRPC R package. Operations operations like these are possible: g.random <- randomGraph (V, M, 0.4) g.random &l ...
written 6.9 years ago by Paul Shannon1.1k

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Centurion 6.6 years ago, created 100 posts.

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