Hi Jackson, I'll take a wild guess at "What is wrong?". You only got one end of the color vector, probably the purple end. As my recollection of principal components analysis is of a data reduction method, you probably have a lot fewer than 500 points on your plot. If you only have, say, 50 values to plot, you will only use up 50 colors. If this is a good guess, you will have to link the colors to the values you are plotting, not the original values. I have very little idea of what either set of values is like, but you may be able to work it out. Jim On Tue, May 24, 2016 at 12:34 PM, Jackson Rodrigues
<jacksonmrodrigues at gmail.com> wrote:
Hi Jim, thank you very much! It seems to be very easy! Another question, how to implement it on ordination? What is wrong? test.pca<-rda(mat5) plot(test.pca, col=agecol,display="sites", cex=1, type="p",scaling=-3) Thank you very much again Jackson 2016-05-23 23:08 GMT-03:00 Jim Lemon <drjimlemon at gmail.com>:
Hi Jackson,
One way to assign colors to values is:
library(plotrix)
ages<-seq(1, 50000, by = 100)
agecol<-color.scale(ages,extremes=c("purple","red"))
Then just use "agecol" for your point colors.
Jim
On Tue, May 24, 2016 at 11:57 AM, Jackson Rodrigues
<jacksonmrodrigues at gmail.com> wrote:
Hi everybody,
I have a big matrix spread over a long time period.
I would like to make a ordination plot (PCA, CA, DCA etc) of this matrix
and look for patterns on time by exploring a color scheme (I have heat
color in mind).
The idea is to use a progressive color scheme ranging from red (the
oldest
age) until purple (the youngest one). Then, make a ordination and see if
the similar colors are plotted together, if so , I would have a pattern
on
time easily identifiable on 2 dimensions.
Let me give an hypothetical case to you.
mat5 <- matrix(rnorm(2000), ,4) #I have a matrix
mat5
seq<-seq(1, 50000, by = 100) # I have a time sequence of 500 dates
ranging
from 50000 to 1
seq
rownames(mat5) <- c(seq ) # making ages the row names of the matrix
library("vegan")
test.pca<-rda(mat5) # Ordination (PCA)
plot(test.pca, scaling=-3) # In this plot I would like to have the old
ages
ranging from red (age 50000) to purple (age 1)
Would that be possible??
Thank you all for any help
Jackson M. Rodrigues
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-- Jackson M. Rodrigues Department of Palynology and Climate Dynamics Albrecht-von-Haller-Institute for Plant Sciences Georg-August-University G?ttingen Untere Karspuele 2 37073 G?ttingen/Germany Tel.: 0049 (0) 176 8186 4994 Web: http://www.uni-goettingen.de/en/306700.html "In order to succeed, we must first believe that we can." Nikos Kazantzakis