similar to: Read in cluster files (cdt, atr, gtr)

Hi, I am making some DNA distances and I would like to use dist.dna as matrix in R, but this command does not include models like GTR... Is there some command or alternative using dist.dna in ape package for models not included like GTR? I would appreciate any help given Thank you very much, Ignacio Quintero Laboratorio de biología evolutiva de vertebrados (Evolvert) Departamento de Ciencias

ok.. Wine : 1.1.3 Game: GTR Evolution - by Simbin Game loads, can select event's, cannot change car's settings, like ride-height etc, as that screen only shows tte arrows and not the information that changes.. goto drive, and it crashes.. Error below.. Code: physics at physics:~/.wine/drive_c/Program Files/SimBin/GTR Evolution Offline$ wine Race07.exe err:module:import_dll

Dear all this is a question of model specification in lme which I'd for which I'd greatly appreciate some guidance. Suppose I have data in long format gene treatment rep Y 1 1 1 4.32 1 1 2 4.67 1 1 3 5.09 . . . . . . . . . . . . 1 4 1 3.67 1 4 2 4.64 1 4 3 4.87 .

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if

Hi, We have a client that is looking for a CPCI or ATR system. If someone from sales could get back to me that would be greatly appreciated. I can be reached at 848-210-0001 or 914-600-2000. Thanks in advance. Regards, Dovid -------------- next part -------------- An HTML attachment was scrubbed... URL:

Hi Allen and list, See the code below.? I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.? All gave the same results.? The problem is in the last line: when I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks!

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks,

Hi, I wanted to make more than one side color bar. For example, I can make one side color bar (col1) with the following code: ----------------------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 ==

I am in a situation needing 3 ColSideColors for heatmap.2. How can I do that? TIA Daren

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is this intended? I expected the following columns to be shifted to the right by sepwidth. Is there a way

Can someone recommend a more sophisticated way to annotate heatmaps than the ColSideColors argument of heatmap and heatmap.2? In particular, I would like to be able to annotate columns with more than one piece of information, like in Figure 1 of the article at http://www3.interscience.wiley.com/cgi-bin/fulltext/117905619/HTMLSTART / doi:10.1002/hep.22256. Some example data and a heatmap:

Dear list, I have a question on moving color keys when side color bars are added to a heatmap. The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? ------ library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x),

Dear list members, I have been using R to create a heatmap where my data has continous variables from 0 to 100. When I create the heatmap, although the branches are correct, they do not order themselves so that the row with the most zeros is at one end and the row with the most 100s is at the other, which is what I would like them to do, so as to create a colour gradient down the graphic. I have

hi lee. I see your problem with trunk iax, probably i don't have the solution but i don't knew if you can help me to solve mine. i want to connecte two asterisk server: server A and server B. i want make possible calls betwen all asterisk users.: users in server A with sip number 022100 can phone another sip user in server B with number 037100. this is my config:

Hi, I want to generate a heatmap for my data (in a matrix). However, the data has some missing values (represented as blank). I get the following errors (with the blanks and with blanks replaced by NA and including the option rm.na = TURE): > filename = "input_heatmap.txt" > g <- as.matrix(filedata) > fg <- rainbow(nrow(g), start=0, end=.3) > gg <-

I'd like to announce the availability of a new library for hybrid hierarchical clustering, "hybridHclust". The library has been uploaded to CRAN and is now available. The library implements a hybrid of top-down and bottom-up hierarchical clustering. Along the way, the idea of a "mutual cluster" is developed. A mutual cluster is a set of observations whose largest

I'd like to announce the availability of a new library for hybrid hierarchical clustering, "hybridHclust". The library has been uploaded to CRAN and is now available. The library implements a hybrid of top-down and bottom-up hierarchical clustering. Along the way, the idea of a "mutual cluster" is developed. A mutual cluster is a set of observations whose largest

Hi, I'm trying to calculate a ratematrix for a RNA aligment (U instead of T) in order to use it as a ratematrix in Profidst (a phylogenetic program which takes into account both the primary sequence and the secondary structure of the RNA, in my case rRNA). The sequence-structure aligment has been made in 4SALE (a java app) and saved as one-letter encoded (using a 12 letters alphabet,

Hello, I recently have try to install GTR 2 in Ubuntu. I have wine 0.9.61 installed in Ubuntu 8.04. Could you help me to solve this problem? If you need more details, I am all yours. neoraptor. When I launch the game (installation is ok), I obtain the following message: > fixme:ntdll:NtQuerySystemInformation info_class SYSTEM_HANDLE_INFORMATION > fixme:ntdll:NtQueryObject Unsupported