similar to: biplot package

Dear all, I've been learning biplot (Gabriel, 1971) and some days ago I sent for this list a procedural function with invitation for a collaborative package. Jari Oksanen made some suggestions and I agree with all. So, I reworked the function under the object-oriented programming (OOP/S3). I think it is now a good frame for more resources. Below it is the function and a small script to

If I perform PCA on the 'eurodist' data, should I get an accurate geographic layout of the cities with biplot? (barring inversions, i.e. their is no way to define north.. but you get the idea...) I have a complex distance matrix, and I am thinking about how to cluster it and how to visualize the quality of the resulting clusters. If I could 'see' the clusters in space I could

> biplot standardGeneric for "biplot" defined from package "stats" function (x, ...) standardGeneric("biplot") <environment: 0x0d4444d8> Methods may be defined for arguments: x Use showMethods("biplot") for currently available ones. > > > showMethods("biplot") Function: biplot (package stats) x="ANY"

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 all I have produced a biplot for a PCA (see attached pdf) that I ran however the names of the variables which are placed at the end of the arrows overlap and are thus unreadable. Similarly some of the numbered points overlap. I was wondering if there was a way to edit the biplot to move the label names and if not what the best alternative is. Thanks Anna pca<-biodata[,3:10]

Dear list, I'm trying to make a biplot, but instead of plotting the row number for each observation, plot a group factor. Example: prcomp(iris[,1:4]) -> PCA biplot(PCA) #this makes a nice biplot but with row names Instead of row numbers I want to plot iris[,5], which is a factor. I can do this: plot(PCA$x[,1], PCA$x[,2], type="n") text(PCA$x[,1], PCA$x[,2], labels=iris[,5],

There is help for grDevices::bringToTop but the function is not present. > bringToTop() Error in bringToTop() : could not find function "bringToTop" > grDevices::bringToTop() Error: 'bringToTop' is not an exported object from 'namespace:grDevices' > getAnywhere(bringToTop) no object named ?bringToTop? was found # help output: > ?bringToTop bringToTop

It's a Windows-only function. It looks like revision r75103 moved it out of the Windows section of the help pages six years ago. Some other help pages were similarly moved, e.g. - ?windows and ?windowsFonts, document the functions as being Windows-only. - ?msgWindow and ?windows.options have the same issue as ?bringToTop. Maybe someone remembers the intention of that move...

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've tried a few things both with prcomp(), and rda() and its friends in vegan (including biplot.rda and ordiplot), but can't find a solution. I'd like to associate subsets of the points in a resulting biplot ("sites" in the rda object) with different plotting colors/text styles to emphasize certain sets of points. I can't figure out how to keep the arrows (for

Hi, I?ve written a script to run several multivariate statistical analysis automatically. As one result a biplot and screeplot is produced. Now I?d like to display the name of the inputdatset as part of the title of these graphics and I do not want to enter it each time I run the script. How can I extract the name of a dataset? An (shortened) extraction from the script: >Test1 <-

Currently (R-2.7.1 on Windows) bringToTop(stay=TRUE) when run before a device is opened, gives the error message > bringToTop(stay=TRUE) Error in bringToTop(stay = TRUE) : can only bring windows devices to the front > In the same circumstances, a call to par() opens a device. My request is to modify bringToTop(). If bringToTop() determines that it is running in an interactive

Full_Name: Henrik Bengtsson Version: R v1.7.1 OS: WinXP Pro Submission from: (NULL) (130.235.2.229) bringToTop() does not work if some windows has been closed. Example: graphics.off() x11() # opens Figure 2 x11() # opens Figure 3 dev.set(2) dev.off() # closes Figure 2 bringToTop(3) # Gives an error # Error in bringToTop(as.integer(which)) : invalid value of `which'

The script below successfully produces a biplot of the data but the 'site names' (rows) and the names of the 'response variables' (columns) are shown as simple numerals (rather than the column and row names). How might I 'enforce' the use of the row/column names used in the datafile (section of datafile shown below)? Can anyone help, please? Section of datafile sample a b

Hi, I am doing PCA on several columns of data in a data.frame. I am interested in particular rows of data which may have a particular combination of 'types' of column values (without any pre-conception of what they may be). I do the following... # My data table. allDat <- read.table("big_select_thresh_5", header=1) # Where some rows look like this... # PDB SUNID1

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:

Hi Listers, I am trying to reflect a PCA biplot in the x-axis (i.e. PC1) but am not having much success. In theory I believe all I need to do is multiply the site and species scores for the PC1 by -1, which would effectively flip the biplot. I am creating a blank plot using the plot command and accessing the results from a call to rda. I then use the calls to scores to obtain separate site and

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

Dear R helpers, When producing a PCA biplot, vectors of environmental variables (as red arrows with labels) and scores of the observations (black labels (observation names)) are plotted by default. How can I change the graphical output? Let's say I would like that the scores are plottet only as symbols and not text. The only solution I found was this post in the help archive