Displaying 20 results from an estimated 2000 matches similar to: "Different labels for subsets of points in a PCA or RDA biplot"
2004 Jul 22
1
biplot & identify
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
2011 Aug 09
2
reflecting a PCA biplot
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
2004 Sep 30
3
biplot.princomp with loadings only
Hi
is there a way to plot only the loadings in a biplot (with the nice
arrows), and to skip the scores?
thanks
christoph
2008 Apr 11
1
Vegan plotting- color help
I have looked all over the internet for being able to color sites
differently in a plot of an MDS (metaMDS)- I would like to color the
different sites in the ordination plot (plot or ordiplot). I have set
the matrix up so that my site code is 1 .... 296 (first column). is
there a way to make 1-23 blue, 24-40 red etc.
thanks
Stephen
--
Let's not spend our time and resources thinking
2010 Nov 23
1
RDA Triplot
Hi
Im using the VEGAN package to do an RDA ordination. In my plot I get my
environmental scores as arrows/vectors, but my species scores as points. I
would like to get the species scores as arrows as well.
I tried the envfit function, and this creates arrows, but the lenght is not
proportionate to the strengh of the correlation and the point is still there
(so I both have point and arrow).
fit
2010 Apr 02
2
Biplot for PCA using labdsv package
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
2002 Sep 09
1
Re: Biplot function of PCA
[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
2012 Apr 25
1
pca biplot.princomp has a bug?
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
2009 Apr 28
1
colored PCA biplot
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]]
2010 Jan 25
1
PCA: Showing file datalabels on biplot
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
2006 Apr 20
2
PCA biplot question
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]]
2010 Apr 27
1
Symbols in biplot
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",
2011 Nov 24
4
I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?
Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account.
I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such
2006 Sep 06
2
biplot label size
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]]
2013 Feb 11
1
Clean up biplot resulting from princomp()
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
2003 Apr 04
2
biplot
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
2010 Aug 14
1
cca biplot (vegan) failed in matplot
Dear List,
I am trying to plot the result of cca using matplot but failed.
Pls kindly help and thanks.
Elaine
The error message was
error in xy.coords(x, y, xlabel, ylabel, log = log) :
(list) object cannot be coerced to type 'double'
code
rm(list=ls())
library(vegan)
library(MASS)
# input richness
birdrich
2011 May 13
2
biplots for PCA
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]
2009 Sep 02
4
"biplot" graphical options?
Dear R-help fellows
good afternoon.
I am struggling in the attempt to impose some graphical conditions (changing point symbols, colors, etc) to biplot function (I am using it to visualize the results of princomp) but I can't apparently manage to change anything but the axis... and I have been browsing manuals and vignettes without finding any explicit suggestions on how to operate...
Can
2012 Jun 18
2
How can I "declutter"/make a biplot less messy in R
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