similar to: Merging graphs with common nodes

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

On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com> wrote: > > On 10/09/2017 11:16 AM, Paul Smith wrote: >> >> I am trying to install >> >> igraph package >> >> but getting the following error: >> >> ------------------ >> make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1 >> ERROR:

Dear All, I am trying to install igraph package but getting the following error: ------------------ make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1 ERROR: compilation failed for package ?igraph? * removing ?/usr/lib64/R/library/igraph? ------------------ Any ideas? Thanks in advance, Paul

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

Hello: I've been trying for days now to get igraph working on a debian sarge install. There does not appear to be any pre-built packages, and when I try and install within R, it blows up on the final linking, claiming its unable to find libgfortran (which IS installed, and IS working for all other users of the compiler). I started up R and ran: install.packages("igraph"). It

Hello, I'm having a look at section 13.1 from SIP Connect v2 doc (see [1]). It refers to RFC6442 which gives the following example (sorry for its length): INVITE sips:bob at biloxi.example.com SIP/2.0 Via: SIPS/2.0/TLS pc33.atlanta.example.com;branch=z9hG4bK74bf9 Max-Forwards: 70 To: Bob <sips:bob at biloxi.example.com> From: Alice <sips:alice at

I realize that matrix indexing has been addressed in various flavors, but I''m stumped and didn''t find anything in the archives. It''s not clear if it is an igraph issue or a more general problem. Thanks in advance for your patience. I am using igraph to read a gml file (http://www-personal.umich.edu/~mejn/netdata/football.zip ). The gml file contains vertex attributes

I'm interested in using R's plotting capabilities to try to generate a graph showing the relationship/pairing frequency of words appearing in a block of unstructured text. I don't have a specific algorithm or approach in mind, just looking to portray text in an interesting fashion. The output I'm hoping for is something like the following called a "Phrase Network":

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

Hi there, How may I smooth spline two vectors with the smoothing parameter selected by generalized maximum likelihood (GML) .? Thanks a lot. -- View this message in context: http://r.789695.n4.nabble.com/Smoothing-spline-with-smoothing-parameters-selected-by-generalized-maximum-likelihood-tp4210679p4210679.html Sent from the R help mailing list archive at Nabble.com.

I have compiled R version 1.3.1 on a Linux system. No errors or warnings are reported. However, "make check" fails thus: ===== make[5]: Leaving directory `/proj/informatics-build/GML/R/R-1.3.1/src/library' running code in base-Ex.R ... ../../bin/R --vanilla < base-Ex.R > base-Ex.Rout make[4]: *** [base-Ex.Rout] Error 139 ===== The base-Ex.Rout being produced at this

Hello, Could you please test the solution at https://stackoverflow.com/questions/45318188/getting-error-in-function-igraph-write-graph-graphml-while-installing-igrap Specifically - install.packages("devtools") library(devtools) install_github("igraph/rigraph") Please let us know if this works Regards, -- Saint Pai On Tue, Oct 10, 2017 at 01:40:53AM +0100, Paul Smith

Dear R-list. I'm doing af logistic analyses using gml. The model explaines variations in Adverse events infections (0 og 1) using age as explanatory variable. model2d<-glm(formula=AEorSAEInfecBac~Age,family=binomial("logit"),data=emrisk) I want to get predictions with 95% confidence limits for age 30 and age 60. I've been reading the "google" and "search

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',

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).

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]]

Estimados compañeros estoy con un trabajo sobre redes pathfinder y quería saber si conocéis alguna librería o función para dada la matriz de proximidades sacar la matriz de la red pathfinder. Un cordial saludo y un mejor año 2013. Juan -- ========================================================= Juan Antonio Gil Pascual Prof. Titular de Metodología Cuantitatíva correo: jgil en edu.uned.es

After writing some code (stupidly without checking to see if there was code to do this already) to generate PostGIS SQL insert statements for simple geometry (wkt), I didn't check see if there is already something available to convert WKT strings into some R package geometry (sp?). Does anyone have any advice, hints, code (?) for converting the following OpenGIS strings into something

Dear R users, I would like to draw map and import it in maptools/spatstat packages. The 'raw data' I have come from a web page (<map>...</map>) and are basically a list of coordinates of a polygon. I would like to know how to import them in R; I checked the maptools packages, but all the examples use existing .dbf files. I just have a (serie of) text file(s) looking like

igraph is a package for graphs and networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. NEW FEATURES: - We use the ARPACK library for graph related eigenvalue problems, like Page Rank calculation, Kleinberg's hub and authority scores, eigenvector centrality, etc. There is also a generic interface if someone wants to use