# heat color on age visible on ordination

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## heat color on age visible on ordination

 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         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: heat color on age visible on ordination

 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 <[hidden email]> 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 > >         [[alternative HTML version deleted]] > > ______________________________________________ > [hidden email] mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: heat color on age visible on ordination

 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 <[hidden email]> 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 <[hidden email]>: >> >> 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 >> <[hidden email]> 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 >> > >> >         [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help>> > PLEASE do read the posting guide >> > http://www.R-project.org/posting-guide.html>> > and provide commented, minimal, self-contained, reproducible code. > > > > > -- > > Jackson M. Rodrigues > Department of Palynology and Climate Dynamics > Albrecht-von-Haller-Institute for Plant Sciences > Georg-August-University GĂ¶ttingen > Untere Karspuele 2 > 37073 GĂ¶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 ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.