similar to: biplot breakdown help

Hi! Is there a way to get biplot and identify to work togheter. Having the output of prcomp I would like to draw a biplot that. Instead of plotting the sample (row-names) names plots some "pch" symbols. (thats easy with xlabs) But now I would like to add using identify the names to only some of the points. I have noticed that both biplot.prcomp and biplot.default does a lot of

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

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 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]

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

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],

hey, im trying hard to display names (given in a seperate variable) instead of "case numbers" in a pca plot (by biplot of a prcomp output). somebody could help me with this? lukas

Hi, I am trying to put together a biplot using symbols and different colours instead of text as points. Someone has previously suggested using this code: PC <- prcomp (iris[,1:4]) lambda <- PC$sdev * sqrt(nrow(PC$x)) plot (t(t(PC$x)/lambda),pch=16,col=as.numeric(iris[,5])) par (new=T) Rot <- t(t(PC$rotation)*lambda) XLIM <- c(-max(abs(Rot[,1])),max(abs(Rot[,1]))) XLIM <-

Hi everyone, I'd like to project two pcas onto one device window. I plot my first PCA: biplot(prcomp(t(cerebdevmat)), var.axes=FALSE, cex=c(1,.1), pc.biplot=TRUE) Now I'd like to project the features of another PCA onto this graph. Any suggestions? I know this is easily done in MatLab but haven't figured it out in R. Thanks, Tanya [[alternative HTML version deleted]]

Dear all, I have a very large dataset (1712351 , 20) and would like to plot only the arrows that represent the contribution of each variables. On the sample below I woild like to plot only the explanatory variables (Murder, Assault..) and not the sites. prcomp(USArrests) # inappropriate prcomp(USArrests, scale = TRUE) prcomp(~ Murder + Assault + Rape, data = USArrests, scale = TRUE)

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

Dears, I've been learning biplot (Gabriel, 1971) and I found the function 'biplot', inside of the package 'stats', useful but, a bit limited. So, I'm thinking to start a colaborative package to enhance this methods to other multivariate methods. In this way, I would like to start it, making public a new function (biplot.pca, still in development, but running) that make

Is there an option to draw concentration ellipses in biplots ? It seems really nice to summarize large number of points of each group. Cheers../ Murli

Dear all here is my data called "rglp" structure(list(vzorek = structure(1:17, .Label = c("179/1/1", "179/2/1", "180/1", "181/1", "182/1", "183/1", "184/1", "185/1", "186/1", "187/1", "188/1", "189/1", "190/1", "191/1", "192/1",

As of R 1.7.0, princomp no longer accept matrices with more coloumns than rows. I'm curious: Why was this decision made? I work a lot with data where more coloumns than rows is more of a rule than an exception (for instance spectroscopic data). To me, princomp have two advantages above prcomp: 1) It has a predict method, and 2) it has a biplot method. A biplot method shouldn't be too

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

Please consider the following PCA example; my.df <- data.frame(A=(x <- rnorm(100,mean=100, sd=10)), B=(y <- x + rnorm(100,mean=10, sd=10))) plot(my.df) my.pc <- prcomp(my.df, center=TRUE, scale=TRUE) biplot(my.pc) my.x <- (my.pc$x)[,1] my.y <- (my.pc$x)[,2] plot(my.x, my.y, type="n") text(my.x, my.y, labels=1:100) Clearly the plots have the same

Hi, I have been using the prcomp function to perform PCA on my example microarray data, (stored in metric text files) which looks like this: 1a 1b 1c 1d 1e 1f ...................................................4r 4s 4t g1 1.2705 1.2766 ...........................................................2.0298 g2 0.1631

I have a decent sized matrix (36 x 11,000) that I have preformed a PCA on with prcomp(), but due to the large number of variables I can't plot the result with biplot(). How else can I plot the PCA output? I tried posting this before, but got no responses so I'm trying again. Surely this is a common problem, but I can't find a solution with google? The University of Dundee is a

Hi, I have a problem with making PCA plots that are readable. I would like to set different sympols instead of the numbers of my samples or their names, that I get plotted (xlabs). How is this possible? With points, i don´t seem to get the right data plotted onto the PCA plot, as I do not quite understand from where it is taken. I dont know how to plot the correct columns of the prcomp