similar to: dendrograms

> hi all, > I am using optim. I am getting the following error message: > > Error in optim(par = start.vals[, h], fn = post.func.pois, gr = post.grad. > pois, : > L-BFGS-B needs finite values of fn > > If I look at optim typing '> optim' it seems that the error comes from > inside .Internal(optim), so I wonder how can I see the code for .Internal(

hello all, I am trying to print a ps file as part of a function as in: func <- function (..., filename="temp.ps") { # some stuff [...] # plot eval( cat("postscript(\"",filename,"\")\n", sep="") ) plot(...) abline(...) dev.off() # more stuff [...] } but it does not work. Nor it does with 'paste' instead

hello, I am using LDA and QDA function of MASS library. I understand Fisher LDA is a method non-probabilistic in nature, so I wonder what happens when I try to predict my test set examples as in: > fit <- lda(labels~., data=train.table, prior=c(.5,.5)) > pred <- predict(fit, data=test.table, prior=c(.5,.5)) Specifically I ask this because in my problem there are 700 examples

Hi, I am using the following R version: > R version 2.4.1 (2006-12-18) > Copyright (C) 2006 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 I believe I found a bug in the 'hist' function, when 'probability=TRUE'. I looked in the archives and I came across problems with the 'hist' functions (e.g., bug PR# 944, posted in 2001), however, a

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

Hello fellow R users, I am currently learning to use R, so please forgive me if there is an obvious explanation for the following problem. My goal is to perform WGCNA on a dataset of 19776 genes, so I opted to follow the block-wise network construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and Steve Horvath. I ended up with 10 blocks and am able to plot the dendrograms and

Ladies and Gentlemen, As Johan Lindberg points out, the documentation for handling dendrograms is sparse....Does anyone know who is responsible for or working on development of tree methods and objects? I've written a couple of scripts for my own use to translate between parenthetical (A(B(CD))) or binary A00 B10 C11 D11 tree formats and cluster objects in R, but as an inexperienced

installed from the binary image (http://cran.r-project.org/bin/ macosx/) on an intel mac 10.4.10 throws three warnings: ----------------- R version 2.5.1 (2007-06-27) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or

Hello there friends & foes, I've had if with M$ windows! Next week I'll sabotage my shop (how 'bout password protecting dualboots on WS) and force LINUX down my users' throats ;-) (oh, don't I like this tone... makes me feel Billy G.) Oops, showstopper! ACL enabled network filesystem, where is it? I can't go with alpha code nfs4, so is there a patch to the smb

I am using hclust and plot to produce dendrograms. Using my input data I am able to complete an analysis and obtain a vertical plot. I want to be able to plot the dendrogram horizontally.I am using version 2.6 of R and have updated my packages recently. Using the sample script for dendrograms I can produce a horizontal plot using the instruction horiz = TRUE in plot(). When I use the same

I would like to be able to exert certain types of control over the plotting of dendrograms (representing hierarchical clusterings) that I think is best achieved by modifying the dendrogram object prior to plotting. I am using the "dendrogram" class and associated methods. Define the cluster number of each cluster formed as the corresponding row of the merge object. So, if you are

hallo i'm running mepis (debian unstable) and if i install wine from the regular (non-wine specific) deb repositories, I get wine 20041019. if I install from wine.sourceforge, I get 200501011. with the former, the application seems to lock up much more often. with the latter, the ability to play the movie (e.g. to see which audio stream to include) is disabled. i see from this screenshot

I'd like to be able to cut dendrograms at a height I specify and then plot the resulting subtrees. I wanted to use the dendrogram object for this purpose because there doesn't seem to be a canned way to cut a hclust object and get a list of hclust objects, but there is a function (cut) that does that for dendrograms. The problem I'm having is that when I plot a dendrogram, I

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite

I added the winehq debian repository to apt-get | synaptic (I am running mepis 3.3) and would like to install those rather than the debian official unstable builds but since the winehq repository is also marked as part of 'unstable' distro I can't find a way to distinguish the wine / winelib provided by winehq from the official ones (which would need the many winelib-* packages)

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph

Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that. _____________________________________________ Patrick Richardson Biostatistician - Program of Translational Medicine Van Andel Research Institute - Webb Lab 333 Bostwick Avenue NE Grand Rapids, MI 49503 ph. 616.234.5787 This email message,

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

Hello, a. when I use hclust with the methods media, centroid, and mcquitty, and plot the results, the dendrograms have lines that are crossing each other. Is this ok? b. My next question refers to plot.dendrogram: How can I use parameters as "hang" or "cex" here? E.g. for st <- as.dendrogram(subtreeshc[[x]]) I would like to have something like this, where cex and hang

Hi, I was wondering if there is more flexibility in the output of dendrograms when plotting a hclust object. I can't seem to find information on how to change the default output of a "hanging" style tree with the axis on the right to a left-to-right plot with and axis on the bottom. Example code follows: library(vegan) #loads the "vegan" module that compuptes ANOSIM