Re: [R] Nodes edges with similarity matrix
Hello, sorry that I interfer, but I tried to do this The SymTest matrix: A B C D E F G A 0.3 0.1 0.5 0.7 0.2 0.8 0.1 B 0.1 0.5 0.4 0.6 0.7 0.3 0.7 C 0.5 0.4 0.3 0.5 0.1 0.1 0.5 D 0.7 0.6 0.5 0.4 0.3 0.5 0.7 E 0.2 0.7 0.1 0.3 0.5 0.2 0.1 F 0.8 0.3 0.1 0.5 0.2 0.3 0.5 G 0.1 0.7 0.5 0.7 0.1 0.5 0.1 g A graphAM graph with undirected edges Number of Nodes = 7 Number of Edges = 28 g - new(graphAM, adjMat=SymTest, values=list(weight=0)) plot(g) Fehler in as.vector(x, double) : kann nicht nach Vektor umwandeln (Error in as.vector(x, double) : can not convert to vector) what goes wrong? Thanks in advance Birgit Am 29.08.2007 um 07:19 schrieb Gabor Grothendieck: Try this: # test data mat - structure(c(1, 0.325141612, 0.002109751, 0.250153137, 0.0223676, 1, 0.342654, 0.1987485, 0.9723831, 0.9644216, 1, 0.7391222, 0.394331, 0.5460461, 0.7080224, 1), .Dim = c(4L, 4L), .Dimnames = list( c(a, b, c, d), c(a, b, c, d))) library(sna) # draw edges according to value gplot(mat, edge.lwd = mat, label = rownames(mat)) # thresholding at 0.5 gplot(mat .5, label = rownames(mat)) On 8/28/07, H. Paul Benton [EMAIL PROTECTED] wrote: Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to convert my matrix to an object that graph can use. my similarity matrix looks like: sim[1:4,] a b c d [a] 1.0 0.0223676 0.9723831 0.3943310 [b] 0.325141612 1.000 0.9644216 0.5460461 [c] 0.002109751 0.3426540 1.000 0.7080224 [d] 0.250153137 0.1987485 0.7391222 1.000 please don't get caught up with the numbers I simple made this to show. I have not produce the code yet to make my similitary matrix. Does anyone know a method to do this or do I have to write something. :( If I do any starter code :D jj. If I've read something wrong or misunderstood my apologies. cheers, Paul -- Research Technician Mass Spectrometry o The / o Scripps \ o Research / o Institute __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nodes edges with similarity matrix
Birgit Lemcke [EMAIL PROTECTED] writes: Hello, sorry that I interfer, but I tried to do this The SymTest matrix: A B C D E F G A 0.3 0.1 0.5 0.7 0.2 0.8 0.1 B 0.1 0.5 0.4 0.6 0.7 0.3 0.7 C 0.5 0.4 0.3 0.5 0.1 0.1 0.5 D 0.7 0.6 0.5 0.4 0.3 0.5 0.7 E 0.2 0.7 0.1 0.3 0.5 0.2 0.1 F 0.8 0.3 0.1 0.5 0.2 0.3 0.5 G 0.1 0.7 0.5 0.7 0.1 0.5 0.1 g A graphAM graph with undirected edges Number of Nodes = 7 Number of Edges = 28 g - new(graphAM, adjMat=SymTest, values=list(weight=0)) plot(g) Fehler in as.vector(x, double) : kann nicht nach Vektor umwandeln (Error in as.vector(x, double) : can not convert to vector) what goes wrong? I suspect that you have not installed and loaded Rgraphviz which contains the code to plot graph objects from the graph package. Without further details, for example the output of sessionInfo(), it is difficult to say. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Nodes edges with similarity matrix
Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to convert my matrix to an object that graph can use. my similarity matrix looks like: sim[1:4,] a b c d [a] 1.0 0.0223676 0.9723831 0.3943310 [b] 0.325141612 1.000 0.9644216 0.5460461 [c] 0.002109751 0.3426540 1.000 0.7080224 [d] 0.250153137 0.1987485 0.7391222 1.000 please don't get caught up with the numbers I simple made this to show. I have not produce the code yet to make my similitary matrix. Does anyone know a method to do this or do I have to write something. :( If I do any starter code :D jj. If I've read something wrong or misunderstood my apologies. cheers, Paul -- Research Technician Mass Spectrometry o The / o Scripps \ o Research / o Institute __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nodes edges with similarity matrix
Paul, i have no idea what functionality you need from graph, but if the igraph package can do what you want then it can easily convert this to a graph for you, basically it is just threshold - 0.5 g - graph.adjacency(simthreshoold) or you can create a weighted graph: g - graph.adjacency(sim, weighted=TRUE) or a weighted graph after a threshold: sim2 - sim sim2[ simthreshold ] - 0 g - graph.adjacency(sim2, weighted=TRUE) etc. Best, Gabor On Tue, Aug 28, 2007 at 02:25:27PM -0700, H. Paul Benton wrote: Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to convert my matrix to an object that graph can use. my similarity matrix looks like: sim[1:4,] a b c d [a] 1.0 0.0223676 0.9723831 0.3943310 [b] 0.325141612 1.000 0.9644216 0.5460461 [c] 0.002109751 0.3426540 1.000 0.7080224 [d] 0.250153137 0.1987485 0.7391222 1.000 please don't get caught up with the numbers I simple made this to show. I have not produce the code yet to make my similitary matrix. Does anyone know a method to do this or do I have to write something. :( If I do any starter code :D jj. If I've read something wrong or misunderstood my apologies. cheers, Paul -- Research Technician Mass Spectrometry o The / o Scripps \ o Research / o Institute __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nodes edges with similarity matrix
Hi Paul, H. Paul Benton [EMAIL PROTECTED] writes: I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to convert my matrix to an object that graph can use. my similarity matrix looks like: sim[1:4,] a b c d [a] 1.0 0.0223676 0.9723831 0.3943310 [b] 0.325141612 1.000 0.9644216 0.5460461 [c] 0.002109751 0.3426540 1.000 0.7080224 [d] 0.250153137 0.1987485 0.7391222 1.000 please don't get caught up with the numbers I simple made this to show. I have not produce the code yet to make my similitary matrix. Does anyone know a method to do this or do I have to write something. :( If I do any starter code :D jj. If I've read something wrong or misunderstood my apologies. The matrix you have can be interpreted as an adjacency matrix where a value of zero means no relationship and a non-zero value indicates an edge between two nodes with edge weight determined by the value. You can create a graph object like this: library(graph) g - new(graphAM, adjMat=sim, values=list(weight=0)) The default is to create an undirected graph and in this case you must provide a symmetric matrix. Generally I would expect a similarity matrix to be symmetric, but the similitary (sic) matrix you have above is not. In this case, you can use a directed graph: g - new(graphAM, adjMat=sim, values=list(weight=0), edgemode=directed) To visualize your graph you can use the Rgraphviz package which will allow you to do: plot(g) You might also be interested in the RBGL package which provides many powerful graph algorithms. All of these packages are available via Bioconductor (no bio required) and can be installed as: source(http://bioconductor.org/biocLite.R;) biocLite(c(RBGL, Rgraphviz)) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nodes edges with similarity matrix
Along with the example I gave using graphAM, you might also want to look at the help page for the distGraph class which may be more directly what you want: library(graph) class ? distGraph __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nodes edges with similarity matrix
Try this: # test data mat - structure(c(1, 0.325141612, 0.002109751, 0.250153137, 0.0223676, 1, 0.342654, 0.1987485, 0.9723831, 0.9644216, 1, 0.7391222, 0.394331, 0.5460461, 0.7080224, 1), .Dim = c(4L, 4L), .Dimnames = list( c(a, b, c, d), c(a, b, c, d))) library(sna) # draw edges according to value gplot(mat, edge.lwd = mat, label = rownames(mat)) # thresholding at 0.5 gplot(mat .5, label = rownames(mat)) On 8/28/07, H. Paul Benton [EMAIL PROTECTED] wrote: Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to convert my matrix to an object that graph can use. my similarity matrix looks like: sim[1:4,] a b c d [a] 1.0 0.0223676 0.9723831 0.3943310 [b] 0.325141612 1.000 0.9644216 0.5460461 [c] 0.002109751 0.3426540 1.000 0.7080224 [d] 0.250153137 0.1987485 0.7391222 1.000 please don't get caught up with the numbers I simple made this to show. I have not produce the code yet to make my similitary matrix. Does anyone know a method to do this or do I have to write something. :( If I do any starter code :D jj. If I've read something wrong or misunderstood my apologies. cheers, Paul -- Research Technician Mass Spectrometry o The / o Scripps \ o Research / o Institute __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
