similar to: Matrix vignette error in June 24 RC

Hi, I installed R-3.1.1 on AIX-5.3 and my installation hanged up while installing Matrix Package. so i killed the gmake ; gmake install the software nad tired installing Matrix package manually - [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]> /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix the package compiled successfully but while loading Matrix package the

Can you please show code example, how to draw graph with some nodes and edges, but with weights. I only found here http://www.bioconductor.org/packages/release/bioc/vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf- Using edge weights for labels, but... Here an example: > library("graph"); library(Rgraphviz) > myNodes = c("s", "p", "q", "r") >

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',

Hi All, After a lengthy battle just to get the package installed, I am not able to actually use Rgraphviz to generate any plots. I tried just using the sample code in the documentation (http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/rgraphviz/) and I get the following: *> > library(Rgraphviz) > test.matrix<-matrix(rep(c(0,1,0,0), 9), ncol=6, nrow=6) >

The package 'graph' defines classes graph and graphNEL (extending graph) and a union,graph,graph-method. These are all exported and fully documented. The package 'GSEABase' Imports: graph and importClassesFrom(graph, graphNEL). GSEABase defines methods on union for its own classes (not graph / graphNEL), and has exportMethods(union). union,graph,graph-method is not used in

Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 1

Hi, I've been using the package "graph" in the BioConductor assortment and writing some functions based on its classes. My question is not specific to this package or BioConductor (I think), but it serves as a useful example. I recently wanted to look at the code for the function "edgeMatrix" for the class "graphNEL". Usually I would type > func.foo and

Dear all, neato makes layouts according to a physical model in which the length of the edges is determined by springs. The weight of the edge is the strength of the spring. However, I was not able to find any influence of edge weight on the layout. In the http://www.graphviz.org/Documentation/neatoguide.pdf the attribute "len" is another parameter of the neato layout. set.seed(31)

On 23/04/2018 6:33 AM, Peter Simons wrote: > Hi, > > I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new > version fails its regression test suite. We configure the build using > the flags "--without-recommended-packages", in case that's relevant. You > can see a complete build log with all relevant information at [1]. > Anyway, the test

igraph is a package for graphs/networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. LINKS Release notes for the 0.5.2 version: http://igraph.sourceforge.net/relnotes-0.5.2.html Release notes for the 0.5.1 version: http://igraph.sourceforge.net/relnotes-0.5.1.html Complete list of changes: http://igraph.sourceforge.net/news.html The

igraph is a package for graphs/networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. LINKS Release notes for the 0.5.2 version: http://igraph.sourceforge.net/relnotes-0.5.2.html Release notes for the 0.5.1 version: http://igraph.sourceforge.net/relnotes-0.5.1.html Complete list of changes: http://igraph.sourceforge.net/news.html The

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef

Hi, I just tried to upgrade Nixpkgs to R 3.5.0, but unfortunately the new version fails its regression test suite. We configure the build using the flags "--without-recommended-packages", in case that's relevant. You can see a complete build log with all relevant information at [1]. Anyway, the test failures look like this: | make[3]: Entering directory

I'm running an Ubuntu 10.04 system and installed R 2.10.1 through the package manger. I then installed Rgraphviz 1.24 and graph 1.26 through R. I'm trying to understand why a complex function my team wrote causes R's memory footprint viewed through top to increase every time it's run. I traced the increase in memory usage to layoutGraph() and wrote the following short function

Hi: My head is spinning with this latex doc so hopefully after I align my tables to the left of the page my headache are going to be over. I always use: \hspace*{-0.1in} to move my figures horizontally to the left margin of the page but the table below doesn't move at all, but instead it gets sideways. Not sure if \begin{landscape} has something to do with it or is just me. I? hope someone

Hello, I have a lot of data and it has a lot of NaN values. I want to compress the data so I don't have memory issues later. Using the Matrix package, sparseMatrix function, and some fiddling around, I have successfully reduced the 'size' of my data (as measured by object.size()). However, NaN values are found all over in my data and zeros are important, but zeros are found very

Good morning, I'm trying to draw a graph, and I'm using the following code. test.matrix<-read.table("~/Desktop/Results/testgephi.csv", header = T, sep=",") colnames(test.matrix) <- gsub("X", "", colnames(test.matrix)) #drop first column drops <- c("") test.matrix<-test.matrix[,!(names(test.matrix) %in% drops)] test.matrix

Using Rgraphviz, I draw the undirected graph with vertices A,B,C and D and edges A:B, B:C, C:D, D:A, A:C. I want the vertices A and B to be red and C and D to be blue. The problem is the following: I want the edges A:B and B:C to be green and the edges C:D and C:A to be yellow, while the edge A:C can have the default colour black. I assume that I have to specify this using the edgeAttrs-argument

Hi- I'm running Vista64 Business and trying to use a package called RGraphViz. Unfortunately, when I try to plot a graph using this package it causes RGUI.EXE to crash. This package has no problem working in WinXP 32-bit. Is there any way to get useful information as to why it crashes? Here's my commands: > library(Rgraphviz) Loading required package: graph Loading required

Dear all, I want to start my post by expressing my sincere gratitude for all the help this group has given me in Sweave/Latex/R. The tools are excellent and so is the community! On to the question. My Sweave code is intended to make lots of plots and create a *.pdf document. Sweave is perfect for this. The only problem is that I find myself using the same R code, within my Sweave input file