similar to: "biplot" graphical options?

Dear BioConductor and R fellow users I apologize in advance for double posting, but I am not sure which list would actually be best fit for this message. I am experiencing a weird error with my R installation on Ubuntu 10.04.4 (LTS) 64bit: When I run R on the terminal everything goes smoothly: $R R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation

Thanks Andris, Michael and Petr for your prompt and kind feedbacks. I will try generating my own biplot from low-level graph commands... I hope it will work. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) PO Box 616 6200 MD Maastricht E-mail: m.manca at path.unimaas.nl Office

Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

Ein eingebundener Text mit undefiniertem Zeichensatz wurde abgetrennt. Name: nicht verf?gbar URL: https://stat.ethz.ch/pipermail/r-help/attachments/20070513/6557c355/attachment.pl

I'm attempting to modify how biplot draws its red vectors (among other things). This is how I've started: Biplot <- function(xx, comps = c(1, 2), cex = c(.6, .4)) { ## Purpose: Makes a biplot with princomp() object to not show arrows ## ---------------------------------------------------------------------- ## Arguments: xx is an object made using princomp() ##

Hi is there a way to plot only the loadings in a biplot (with the nice arrows), and to skip the scores? thanks christoph

Hi everyone, I am doing PCA with labdsv package. I was trying to create a biplot graphs in order to observe arrows related to my variables. However when I run the script for this graph, the console just keep saying: *Error in nrow(y) : element 1 is empty; the part of the args list of 'dim' being evaluated was: (x)* could please someone tell me what this means? what i am doing

Full_Name: Hinrich Göhlmann Version: 1.4.1 OS: Windows 2000 Submission from: (NULL) (148.177.130.121) Hi all, I've searched the known bugs and hopefully I did not oversee this one... When I have done a normal zz<-princomp(na.omit(raw.data)) and I then draw a biplot with biplot(zz,cex=c(.1,.7),col=c(5,1),choice=c(1,2),xlim=c(-2,2),ylim=c(-5,2)) the x axis gets set properly, but the y

Hi everyone. I performing a simple PCA using the princomp function. Then, I use the biplot function to show it. However, the function use line number to represent samples. I would like to know if there's a way to use a dot (point) instead of the line number when using the biplot function. With regards, Phil -- View this message in context:

Dear list, I want to perform a biplot, using customized titels for the x and y axis. Setting xlab="" and ylab="" resulted in an error, e.g.: > data(USArrests) > biplot(princomp(USArrests),xlab="",ylab="") Error in biplot.default(t(t(scores[, choices])/lam), t(t(x$loadings[, : length of dimnames[1] not equal to array extent > How do I

Dear R-helpers, The vectors in my biplot are completely obscured by the ~1400 labels R is printing on my biplot. I don't really care about the labels. How can I make the biplot without the annoying labels? See attached, if that helps you see my problem. Many thanks, Mark Na

x=rmvnorm(2000, rep(0, 6), diag(c(5, rep(1,5)))) x=scale(x, center=T, scale=F) pc <- princomp(x) biplot(pc) There are a bunch of red arrows plotted, what do they mean? I knew that the first arrow labelled with "Var1" should be pointing the most varying direction of the data-set (if we think them as 2000 data points, each being a vector of size 6). I also read from

I am doing a principle component analysis on a dataset with a lot of different variables and have constructed a biplot of the data. Unfortunately, as can be seen on the attached image, the biplot is very messy, cluttered, and hard to read. I have performed a few modifications including outlier removal from a few of the variables, which has made the plot better, however it still is too cluttered

Which is the parameter that is used to decrease the size of ylabs plotted in biplot? I tried playing with cex and cex.lab I am not getting it right pc <- princomp(USArrests) biplot(pc, xlabs = rep("", nrow(USArrests)),ylabs=(colnames(USArrests))) Thanks../Murli [[alternative HTML version deleted]]

Hello everybody, I am afraid this might be a stupid question, but after scanning a little bit through the help archive and the internet, I didn't come up with an answer myself. I have done a principle component analysis on a data set, which yields the mean response of 14 olfactory neurons to 16 different odors. When plotting the result in a biplot, it nicely shows me the odors in

Hello, I have a graphical problem concerning a biplot that I was ask to insert in a scientific work to be published. I've performed a princomp analysis and produce the relative biplot but the labels of variables are out of margin (see attached file). When I try to wide the x axis by the function xlim=c(i:j), nothing happens if not a partial shift of the x range. Is there any specific

Hi- I'm trying to make my PCA (princomp) colored. In my csv excel sheet, I have the first column numbered according to the groupings I want to assign to the PCA. I've played around with trying to set this first column as the color vector, but haven't had any luck. Any suggestions? Thanks, Hillary [[alternative HTML version deleted]]

Hello all, I just started in on R today. I am at the point where I am trying to distinguish different groups of data (hydrochemical data) in biplot. I search and found a post about converting the sample number in biplot to a symbol like x or + "> temp <- matrix(runif(50), nrow=10) > temp.pca <- princomp(temp) > biplot(temp.pca, xlabs=c("A", "A",

[was sent a wrong R-help address; manually resent by MM] Hello I'am using the 'biplot' and 'biplot.pincomp' functions of the 'mva' package for my studies. The biplot represents both the observations and the variables of a matrix of multivariate data on the same plot. The observations are represented by their numbers (the line of the data matrix), but I would need to

Hi everybody, Excuse me for this silly question, but after searching the help archives I'm still unable to find my way to read the source code of the "biplot" function in R. I have installed the mvbutils package, and tried: > fixr(biplot) which only gives me: function (x, ...) UseMethod("biplot") with no further details.... I'd like to read the code to see if