User: Nishant Gopalakrishnan

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Posts by Nishant Gopalakrishnan

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Answer: A: bug in rendering reciprocal edges?
... Hi Wouter, Please change the position of the call to the layoutGraph function in your render function as follows and you shall see the reciprocal edges with color and line width render <- function(graph) { nodes = union(graph$subject, graph$object) edges = tapply(graph$object, graph$subje ...
written 8.0 years ago by Nishant Gopalakrishnan340
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Comment: C: GRanges nearest problem
... Hi Arne, Thank you for pointing out the error. I have checked in some changes to fix this issue. Nishant On 04/14/2011 06:21 AM, Valerie Obenchain wrote: > Hi Arne, > > Thanks for pointing out these bugs. I'll post again here when they > have been fixed. > > Valerie > > & ...
written 8.3 years ago by Nishant Gopalakrishnan340
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Answer: A: flowTrack error: package ‘flowTrack’ is not available
... Hi Louis, What version of R were you using ?. I believe that script will install flowTrack if you have R version 2.11 Nishant On 04/01/2011 06:39 AM, Louis Peperzak wrote: > Goodday, > I tried to install flowTrack following Gopalakrishnan (2010) once, and a second time after setting the ...
written 8.4 years ago by Nishant Gopalakrishnan340
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Answer: A: graph classes: how to combine multiple graphs into a single graph
... Hi Paul I believe that you had posted this question on the mailing list before and I had responded to it here https://stat.ethz.ch/pipermail/bioconductor/2010-December/036706.html The only change made to the graphBAM class (which supports the kind of attribute preserving behavior you are looking ...
written 8.5 years ago by Nishant Gopalakrishnan340
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Answer: A: node-edge connection
... Hi Chris, I tried some of the different options for the layoutType argument for the layoutGraph function in your graph example and was able to get something that was more reasonable to interpret. Perhaps you could try out this code testNet<-ftM2graphNEL(cbind(rep("centre",100),paste("outer",1 ...
written 8.5 years ago by Nishant Gopalakrishnan340
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Answer: A: names of edges in graph classes
... Hi Paul, I am not sure why the edges are named in two different ways. The "| " character is reserved as an edge separator and node names cannot contain "|". It looks like you are right that they should have had a consistent naming schema. Nishant On 01/04/2011 06:13 PM, Paul Shannon wrote: ...
written 8.6 years ago by Nishant Gopalakrishnan340
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Comment: C: graph::join discards node and edge attributes
... Hi Paul, The new graph classes are already available in the graph package for testing. There is also a vignette MultiGraphClass.Rnw that runs through some examples in using the graphBAM and MultiGraph classes to get you started. Nishant On 12/01/2010 01:55 PM, Paul Shannon wrote: > Hi Nishan ...
written 8.7 years ago by Nishant Gopalakrishnan340
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graph::join discards node and edge attributes
... 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 graphUni ...
graph process written 8.7 years ago by Nishant Gopalakrishnan340 • updated 8.7 years ago by Paul Shannon1.1k
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Answer: A: flowStats quadrantGate and 'names'
... Hi Aric, I am not sure what 'names' function in flowViz you are talking about. I do not see one in flowViz. Its hard to guess what you have done without providing some reproducible lines of code. With regard to putting in custom labels inside the plots. (if that?s what you are trying to do) FlowVi ...
written 8.9 years ago by Nishant Gopalakrishnan340
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Answer: A: FlowCore/FlowViz issues
... Hi Roger, Answers to your questions are posted below. Nishant 1) Gating with an ellipsoidGate Is there any explanation regarding how to construct a covariance matrix from the actual dimension I want ?. Is there an alternative constructor to create a gate from real dimensions? Ans: As mentioned ...
written 8.9 years ago by Nishant Gopalakrishnan340

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