similar to: save the layout using igraph

Dear R users, I am trying to draw a network using igraph package. I intend to place the hub nodes (the ones with the relatively more connection with other nodes) in the center of the graph. Also, the graph need to be in the fashion that the higher the correlation between two nodes is , the closer the two nodes will be. Is there any layout that can help or any other way to do this? Thanks in

Hello there, I am using the igraph package to build graphs from my data. If I plot a graph though, it's not easy for me to see what's going on. Does anybody know how to rearrange a graph to get a plot without too many crossing lines? Maybe other packages? Thanks a lot in advance for any pointers, -- D --------------------------------- [[alternative

Hey, I am trying to make a data frame and the name of a column is composed of a number, a dot, and a word, such as "1.whatever". But I always get this error message:"syntax error, unexpected SYMBOL, expecting ',' in:" while printing data frame out . When I rename the column with purely letter, everything works fine. Some suggestion about the cause/ solution ?? Thanks.

Hi R users, I am wondering if it there is any R's function helping integrate venn diagram and pie chart to compare two related datasets. I know the package limma(bioconductor) has something built-in for making venn diagram, but I guess it would be very painful to use line and text to specify the proportions in the fashion of pie chart . Thanks in advance, Kevin Chang -- View this

Hi all, Since proc.time return three different kind of times (user, system and elapsed) , I am wondering which one is right for calculating flops. In New S Language (Becker et. al. ) , it seems to be the user because " the user time measures the processor time used in S and the system time measures the operating system in response to S's request". But in R Help , system time

Hi All, I am trying to rearrange alphabetically each element in a character vector. ex: say the first element in the vector is "cba", and my goal is to turn it into "abc". The suggested function to use is sort(). But it turns out that sort doesn't work at the level of element. So I am wondering that if there is an alternative function for this purpose. Please help me out .

Hi, The loop I wrote executes correctly but is stalled seriously. Is there a way to hasten execution without coming up with a brand new algorithm ? please help. Thanks. -- View this message in context: http://www.nabble.com/stalled-loop-tf4451301.html#a12699524 Sent from the R help mailing list archive at Nabble.com.

Hi R users, I am trying generate the indices for locating a in the string it come from. Given the length of the string, it will take too long using the combn() for further comparison. I am wondering if R has any built-in function for this purpose. To make it concrete: this.substring="cc" this.string="ccc" start.location=1,2 end.location=2,3 Thanks in advance, Kevin

I am using 'igraph' package to make some graphs of 'gene-gene interaction'. I can get a data.frame which has three columns. gene1 gene2 pvalue AGT MLR 1.2e-04 MLR 11BHSD1 1.71e-05 IFG2 11BHSD2 2.2e-07 . . . . . . . . . AGTR1 NPPA

Hi, I have a erdos-renyi game with 6000 nodes and probability 0.003. g1 = erdos.renyi.game(6000, 0.003) How to create a Watts Strogatz game with the same probability. g1 = watts.strogatz.game(1, 6000, ?, ?) What should be the third and fourth parameter to this argument. -- View this message in context: http://r.789695.n4.nabble.com/Watts-Strogatz-game-tp3491922p3491922.html Sent from the R

Hi, I am plotting degree distribution of a graph using the function, library(igraph) dd1 = degree.distribution(G) plot(dd1, xlab = "degree", ylab="frequency") I would like to plot the mean of the distribution as a vertical line in the attached plot. Please let me know how to do this. Thanks, Kumar http://r.789695.n4.nabble.com/file/n3334375/cdata3_dd.png cdata3_dd.png --

Hello all, I'm having a spot of trouble. I have made a very nice distance matrix from some comparison calculations. However, the matrix is 3096 x 3096, so it's relatively large. Currently I'm using the svn package as it seems to work for my data. The graph package errors and says the "adjacency matrix must be symmetric for undirected graphs". I though 3096 x 3096 was

Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to

I'm new to R and igraph and I was wondering if anybody can help me with the following. I want to find the edge weight between two vertices in a graph. My graph structure is defined by the normal ego (node1), alter (node2) and the weight of the edge between them. I know that I can get the weight for each of the edges in the list of edges that originate from node number 5 using

**Hi, I wanted to create a network of drugs that are being studied together. So, I created a file as a graph. But plot of my network is not corect! It looks like to me that something else is lying behind this network links created. Could someone help me with this? Thanx! a<-read.graph(file=file.choose(), format="edgelist") plot.igraph(a) File (number present ID of drug): 15 2 10

I have a graph with edge and vertex weights, stored in two data frames: --8<---------------cut here---------------start------------->8--- vertices <- data.frame(vertex=c("a","b","c","d"),weight=c(1,2,1,3)) edges <-

I'm very sorry, but I cannot find any way to send you my bug report. (The email account samba-bugs is disabled, while it can be found on the web page http://de.samba.org/samba/bugreports.html) Can you please send my bug report to the right place, or tell me what should I do to send it to the right person? Thank you very much! Bogdan Zavalnij system administrator ---------- Forwarded

Hi all, I''m playing with the new RJS stuff. Very cool! But I have a problem. The following code works ok: page.select(''div.blogcomment'').each do |element| page.visual_effect :highlight, element end All div''s with class blogcomment are highlighted correctly. But I just want the last elemen to be hightlighted. The following code is not working:

We''re building our first Rails app and looking for a consistent way to provide feedback messages; things like success messages like "your password changed successfully" or form errors with the form field highlighted in red (you know). I''ve read that Rails provides a framework for this but we''ve diverged in how we do this in our app and would to reign things in

Hi! The following Python code does what is excepted under Linux: >>> from ogg.vorbis import * >>> com=VorbisFile('01.ogg').comment() >>> com['title']='foo' >>> com.write_to('01.ogg') but under Windows I get the following error: Traceback (most recent call last): File "<stdin>", line 1, in ? IOError: [Errno