similar to: "reversed" dendogram

Dear all, I am having a problem using grid when rotating a viewport. It seems to plot everything on a grey background colour which I am not able to get rid of. Even book examples such as that that plot figure 5.10 in P. Murrell's R Graphics book show the same behaviour. The following example illustrates this issue. I would appreciate if anyone has a way to solve this. Best regards,

Hi, I am using R 1.9.0 (2004-04-12) for Mac OS X. I am having trouble printing to a jpg file. This only happens when I use R in batch (with the BATCH option) mode. If I launch the R GUI or the command line version and run the script from either, I have no problems. Only when running in BATCH mode I get a file with the same name as my script where I find the following message at the end:

Dear community, I am writing a wrapper for '[' operator, which is a generic method declared as function(x, i, j, ..., drop). It turns out that I need to parse the '...' argument and this is where I am stuck. Generally what I need is the following. Say the call is obj[1, 1, 1:10, 3] - here '1:10, 3' is passed into '...'. What I need to evaluate that '...'

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]]

Dear community, this is just a suggestion, but might be useful for the following R releases. I was programming some C code for R and my compiler constantly showed me some crazy messages that a stdc++ macro length() was supplied with 4 arguments whereas only one was required. The problem could be partially resolved by changing the order of includes. However as soon as the file was used from

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) >

I am using R for hierarchical clustering of a number of documents. I have a distance matrix on which I have applied hclust method. When I plot the result of hclust method, I can see the dendogram plotted. What I need now is the dendogram stored as a tree in a data structure. My goal is to automatically label all internal nodes. For that, I need to know, which leaf nodes make a first level

Dear all, the 'inline' package was updated to version 0.2.2 with the following changes: - functions declared using 'cfunction' can now be saved, the code is recompiled when the object is loaded (not yet implemented for setCMethod) - full path to the R binary is used for compilation allowing for the use of the correct R version when several are installed The

Dear R I recently performed a cluster analysis. It produced the dendogram no problem but unfortunately the font size of the row.names were all cluttered due to their large size So I tried to change the font size using plclust(cluster.results, labels=iris$specie, cex=0.8) and R came back to me saying Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) : unused argument(s)

Dear lists: I am somewhat puzzled by the use of texi2dvi/pdflatex in R2.7.0. When building EBImage (bioconductor) with 2.7.0 I get the same error both in Windows and Linux, which reads the following: ** building package indices ... * DONE (EBImage) * creating vignettes ... ERROR /usr/bin/texi2dvi: pdflatex exited with bad status, quitting. Error in texi2dvi(file = bft, pdf = TRUE, clean =

Hi, I do not know if everybody finds index pages of the html-formatted R help useful, but I know I am at least not the only one who uses them extensively to get the overview of functions and methods in a package (even for my own package). Problems arise, however, if a lot of S4 methods need to be documented blowing out the index with (generally irrelevant) entries like:

Hi everyone It looks like repeated runs of fastICA produce quite significantly different mixing matrices (not only in terms of sign and row order). I'm not a specialist, so would appreciate any advice on whether this should really be the case: > res3 = > fastICA(af[,2:20],4,alg.typ="parallel",fun="logcosh",alpha=1,method="C",row.norm=TRUE) colstandard >

Dear R developers, I am writing some C code that loads multiple images into a list of R matrices. The whole R object is created within the C code. To simplify coding, elements of the list are first created as vectors and then converted to corresponding matrices using setAttrib(x, R_DimSymbol, s). Generally the code works fine except for one detail. Applying setAttrib sets ALL elements

Dear John Fox and everyone, I have been using the effects library with glms and have found it very useful. Now I'm trying it with lms and I'm not sure if the results of the allEffects() are as expected. I've got a model that looks like this: mymodel = lm(formula = A ~ B + C + D + B:D + C:D) Residuals: Min 1Q Median 3Q Max -3.80156 -0.73486 -0.09792

I have used heatmap to visualize my microarray data. I have a matrix of M-values. I do the following. #The distance between the columns. sampdist <- dist(t(matrix[,]), method="euclidean") sclus <- hclust(sampdist, method="average") #The distance between the rows. genedist <- dist(matrix[,], method="euclidean") gclus <- hclust(genedist,

Hi, I have an S4 class directly derived from 'array' as shown in the code below (EBImage package of Bioconductor 2.1, devel), it simply contains array adding a couple of slots: setClass ("Image", representation (colormode="integer", filename="character", compression="character", resolution="numeric", features="list" ),

Any idea why CHAR(asChar(STRING_ELT( produces NA whereas CHAR(STRING_ELT( gets a pointer to a string? It's generally expected that STRING_ELT should already be a character, but why the coercion does not work? Here is a simple example (consistent over R2.5.1-R2.6 rev 42284, I didn't check earlier versions, but it used to be different in 2.4): install.packages("inline")

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!!!

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 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)