similar to: heatmap and phylogram / dendogram ploting problem

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Dear all, I'd like to introduce a new R package called *phylogram,* for working with evolutionary trees as deeply-nested lists known as "dendrogram" objects. The package provides functions for importing and exporting phylogenetic trees in the Newick parenthetic text format, as well as several functions for command-line tree manipulation. With an emphasis on speed and computational

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

Dear All, I am trying to find a way to plot a dendogram in reverse, that is, if the terminal leaves are labelled 1-10 bottom to top (or left to right), I would like to be able to plot it in a way such that if would display 10-1 bottom to top or left to right. Any idea how to achieve this? Thanks in advance, r. Dr. Rafael Najmanovich European Bioinformatics Institute Wellcome Trust

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) >

Dear all, I need to make dendogram from read count in a csv file across 34 samples including biological replicate. Please share R code or package to do this. Do I also need to normalized read count before using read data? Thanks [[alternative HTML version deleted]]

The data "one" is a vector of 553 observations agglone<-agnes(one, metric = "manhattan", stand = TRUE) plot(agglone,which.plots=2, nmax=150) My problem is in the dendogram, I can not see the nodes because it is too crowded. I have attached the diagram. Any help is more than welcome. Thank you a lot!!!

Dear All, I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames)

http://r.789695.n4.nabble.com/file/n2260087/%E6%8D%95%E8%8E%B7.png I am going to plot my data set like this, with means and 25% & 75% quentiles. I've tried "boxplot", but the output is not what I want. Should I use other functions? Thanks -- View this message in context: http://r.789695.n4.nabble.com/ploting-dots-with-quentiles-tp2260087p2260087.html Sent from the R help

I'm trying to do something very simple... I wan to plot a histogram where the y axis represent the percentage of the total sample that each bin represents. I know how to plot a histogram with the counts and density... but can't find anything that gives me perenct of sample on the y axis. Any help is appriciated Below is the script I'm working with par(mfrow=c(1,2))

hi: Yesterday I post a message about hoy to plot a time series, but someone told me to post more information about the file so here it is: the file was read using read.table and the name is list. When I use str(list) it tells the following variables: YEAR int: 2003,2003,2003....2004 MONTH int:1,1,1,1,.... DAY:int 1,1,1,... STATE: factor with 51 levels. SALES: int (sales per day) The reason why

Dear all, I would like to draw a 3-D horizontal cylinder preferably in RGL device (because this gives the look from different angles). Basic idea is from http://www.tau.ac.il/cc/pages/docs/sas8/insight/chap18/sect3.htm. Below is the description exactly what I want to do. Please see at figure 18.6, 1st plot. Here it is an confidence ellipsoid. Suppose now you put another 4 same ellipsoids on top

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this is the command i made for a normal distribution, but when i try to plot the histograms, i dont know why the bars don't stick on the line... nsamples<-1000 sampsize<-15 Samples<-matrix(rnorm(nsamples*sampsize,0,1),nrow=nsamples) a<-apply(Samples,1,var) NC14<-a*14 x<-0:40 plot(x,dchisq(x,14),type='h') hist(NC14,freq=F,add=T) -- View this message in context:

Hi, I would like to be able to develop a function to plot an igraph object with lattice (trellis type displays will be usefull for grouping etc). Anyway, I mostly feeble Igraph requires that you convert two columns of data two an igraph object and to be able to plot the graph...I have tried a very, very simplistic (if not naive) approach and surprise, surprise, it didn't work. First of all,

Hello! I have such a problem... Estimated a model based on common data (you can find it in R library), and I wanted to plot the orginal values with the estimated one. Unfortunately I can only see the original values. Below is the code with data library: / library(forecast) data(AirPassengers) AP <- AirPassengers class(AP) start(AP) end(AP) frequency(AP) lgAP <- log(AP) t<-2:length(AP)

Hi, I've written a function: myfun <- function(x, y) { // blah blah } and I want to graph it. My plan is to use persp(), and my question is: how do I create the array of values? One possibility is: x <- seq(0, 10, by=.1) y <- seq(0, 10, by=.1) inputs <- <somehow create an array of x,y pairs> outputs <- apply(A, c(1,2), myfun) The "inputs" array would

Hi: I been having a lot of trouble trying to plot multiple time series on the same plot. What I want to do is the following: I have a table with sales per day on different states and what i would like to do is plot time series for all the diferents states in the same plot (divided in small squares, not all the time series together) so I can visualize the data; but I do not know how to do this, im

I'm trying to understand how to set graphical parameters for trees created with the party package.  For example take the following code:   library(party)     data(airquality)     airq <- subset(airquality, !is.na(Ozone))     airct <- ctree(Ozone ~ ., data = airq,                    controls = ctree_control(maxsurrogate = 3))     plot(airct)   My problem is, I've got a ctree that has

I used in previous versions of R (R 1.1) to plot axes on projections of factorial coordinates using the function plaxes. This doesn't exist any more. Why this change ? No alternative ? --------------- Charles RAUX, Laboratoire d'Economie des Transports CNRS-Universit? Lumi?re Lyon 2-ENTPE email : charles.raux at let.ish-lyon.cnrs.fr http://www.ish-lyon.cnrs.fr/let