search for: cytoscape

Hello, I am exporting a graph in "gml" format from igraph 0.5.5. When I open the file in Cytoscape v.2.7 I can't map the color attribute that I assign to the graph when I export it from igraph. Could anyone help me in this? Thanks. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg Tel: +49-6221-5451354 [[alternative HTML version deleted]]

Hi,all, I have a problem about launching SJava in R from external application (Cytoscape). My R version is 2.1.0 and Sjava version is 0.68. R is installed by issuing 1. configure --enable-R-shlib 2. make 3. make check 4. make install SJava is installed by issuing "R CMD INSTALL -c SJava_version_.tar.gz". The LD_LIBRARY_PATH is set in .bash_profile by "...

Hello Everyone! This is my first post to the mailing list so please forgive me if I am a bit deflected from the general format of this mailing list posts. Since I need help in this matter urgently, I would cover up any of my mistakes in posting later. That said, I have a problem in merging 2 graphs that have common nodes between them. I have a graph G1, that have nodes N1 and edge set E1 and

Hi, I'm trying to use the XML-RPC client in the SSOAP package to connect to a service that I have created. From other languages (Perl, Python, Ruby) this is not a problem but the SSOAP client gives the following error: Error in .XMLRPC("http://localhost:9000", "Cytoscape.test", .opts = list(verbose = TRUE)) : Failed to parse XML-RPC request: Content is not allowed in prolog. It looks like the SSOAP XML-RPC client is not creating the right type of XML-RPC message. Does anyone know how to fix this or has successfully used the SSOAP XML-RPC client? Thanks, J...

Hi Can some one please point out where i am wrong. I am trying to position set of nodes column-wise in cytoscape using RCytoscape A----D B----E C----F ------------------- g <- new ('graphNEL', edgemode='undirected') cw <- CytoscapeWindow ('smallExample', graph=RCytoscape::makeSimpleGraph()) layout (cw, 'jgraph-spring') redraw(cw) nodesFr = c('A', 'B', &...

I have a large correlation matrix that I'm trying to convert to a list of every connection (edge) between every two nodes with its accompanying correlation value (for Cytoscape). I figured out how to do this and to remove the connections that nodes have to themselves but I can't figure out how to get rid of the duplicate pairs (e.g. the edge b-a is a duplicate of a-b). NodesRow<-rep(c("a","b","c"),each=3) NodesCol<-rep(c("a...

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

Hi there, I need a network builder and it can change the node size and color; I am not sure if network package in R can do this or not. The other functions I wanted have been found in that package. BTW, if there is another package in R relating to this, please suggest too. Thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist "Did you always know?" "No, I did not. But I

...ubilantbiosys.com<mailto:Ekta_Jain@jubilantbiosys.com>> wrote: Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Hi Ekta, If you mean visually, as Steve suggested, you could try packages like ggbio, Gviz, Rcytoscape.. it depends on how you plan to visualize your data, track-based? circular view? net work? and what format your data are? for example, in ggbio, it depends on what data you are using, you can arrange your data into GRanges manually or just provide data that rtracklayer supported like bed, then ju...