similar to: hclust and ggplot2

I'm trying to reproduce the 3rd graph on the page of this site: http://learnr.wordpress.com/2009/03/17/ggplot2-barplots/ . However, the data below produces a ggplot with the stacks sorted in alphabetical order from the bottom up. I'd like the stacks to be in the order "Europe", "Asia", "Americas, "Africa", "Oceania". Is there an easy way to

Hello, The following code does'nt work for me. The last command reports an error. I have created a consensus tree using the consensus comand from phylo but cannot manipulate the phylo object afterwards to create a dendogram , by transforming the phylo object into a hclust object and then into a dendogram ?? Thanks for any help library(ade4) library(cluster) library(stats) library(ape)

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me

Hello all, I'm now working with hclust objects and was hoping to perform some basic editing on them like: - Joining = the merging of two hclust objects (so they will share one root) - Splicing = So to cut/extract a branch out of an hclust object - that by itself will be an hclust object. I noticed I could extract one element of an hclust object by turning it into a dendrogram,

Dear MCMCglmm users, I am currently struggling with the specification of a proper prior and model formula for a multi-response MCMCglmm with two of the three response variables being Gaussian and the third being za-poisson. The model includes several fixed effects and three nested random effects. In general, I would prefer to fit a model with a fixed effect of trait and suppressed intercept for

Hello, I have a C++ code for 2D random walks with traps and I want to convert it in a R code with its syntaxs, can anyone help??????? It's easy for me to adapt the body but I want help with the beginig (variable declaration) and th end exporting the output to a file ( like write.table() or sink() ) Thank you... #include <iostream> #include <math.h>#include

Greetings All, I'm stuck and would appreciate some help. After writing a function to generate a random sample from vector "rand1": > f<-function(i) {y<-sample(rand1,296,replace=F)} and using the function to generate multiple samples from rand1 and store the results in list "l": > l<-lapply(1:100,f) I can't get the next step accomplished; I'd like

I'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data

Hi everyone, i've been trying to make a special plot with ggplot2, but I can't get it to fill the polygon I'd like to see filled so very very much. I want to display the difference or change in the distribution of the modified Rankin Scale between two groups. mRS is a scale for disability or daily activities competence. It looks like this.

On 27/07/16 10:33, hy wu wrote: > > Here is my smb.conf: > > [/usr/local/samba/var] # cat /etc/config/smb.conf > [global] > > client schannel = false > server schannel = false > client ipc signing = false > client signing = false > server signing = false > winbind sealed pipes = false > require strong key = false > > passdb backend = smbpasswd >

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

Hi list, This is my domain enviroment and all DC are windows 2008r2 http://i.imgur.com/8cNOtm2.jpeg When I used samba-4.0.5, I join my box to domain "HC1" , I got trusted domain "CHILD2" in "wbinfo -m". [/share/Public] # wbinfo -m BUILTIN MYBOX HC1 CHILD1 TREEROOT HC2 CHILD2 Then I upgraded my box to samba-4.4.4, I lost CHILD2 in "wbinfo -m".

Hi, Use `check.names=FALSE` head(dd,2) #? Phylo.Tree Genesis.Tree #1????????? 1??????????? 2 #2????????? 2??????????? 3 ?dd <- data.frame("Phylo Tree"= c(1:10), "Genesis Tree"= c(2:11),check.names=FALSE) head(dd,2) #? Phylo Tree Genesis Tree #1????????? 1??????????? 2 #2????????? 2??????????? 3 write.csv(dd,"Crish.csv",row.names=FALSE) ?yy<-

Hi all, I'm having a problem where by I'm trying to use the NeatMap draw.dendrogram function as it is more versatile in placement/direction of dendrograms, instead of the limited plot function. Using plot I can get my dendrograms to display the species name for each leaf of the tree. But I cannot figure out how to make this happen using draw.dendrogram.. genetic<-

Here is my smb.conf: [/usr/local/samba/var] # cat /etc/config/smb.conf [global] client schannel = false server schannel = false client ipc signing = false client signing = false server signing = false winbind sealed pipes = false require strong key = false passdb backend = smbpasswd workgroup = HC1 security = ADS server string = encrypt passwords = Yes username level = 0 map to guest = Bad User

Dear All, I get some problems using the 'phylo' and dissimilarity functions in R. I converted an output from 'hclust' into an order of phylo so as to be able to use the 'consensus' function on it. Each time I submit the consensus codes, my computer hangs. When I tried to see what the contents of the object converted into order phylo is, I get the message

Hi, I would be very grateful if anyone could give me a bit of help with this. I am trying to run Samba 3.0.5, as distributed with Mac OS X server 10.3.8, on an Apple Xserve. Things were working beautifully until I had problems with an IP address change and had to reinstall everything. At present, the situation seems to be that the smb protocol is operating, since I can make an smb

On 27/07/16 09:35, hy wu wrote: > Hi list, > > This is my domain enviroment and all DC are windows 2008r2 > > http://i.imgur.com/8cNOtm2.jpeg > > When I used samba-4.0.5, I join my box to domain "HC1" , I got trusted > domain "CHILD2" in "wbinfo -m". > > [/share/Public] # wbinfo -m > BUILTIN > MYBOX > HC1 > CHILD1 >

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

Hi, I was recently splitting some massive phylo class objects with extract.clade() and noticed what appears to be a bug in how tip labels are copied from the full tree to the pruned tree. This possible bug was also mentioned here: http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html An example: library(ape) set.seed(5) x <- matrix(rnorm(100), ncol=10) p <-