Hello everybody,
I Would like to get some help to plot together, Principal Components
Analysis (PCA) and clusters.
I am handling environmental data from 25 locations spread across 5
different ecosystems.When grouped into 5 clusters, locations from different
ecosystems are arranged in the same group.
So, I want to plot together PCA and Clusters, in a such way that locations
belonging to the same ecosystem are displayed with the same COLORS, and
locations grouped in the same cluster, have the same SHAPE. For example:
I have 1 site from Savanna and 1 site from Serengeti that are in the same
cluster, Thus I would like to plot both with different colors blue and
green, respectively due different ecosystem classification and with the
same shape (triangle) because they are in the same group. So, I would have
a cluster with 2 triangles one green and another blue.
How to make this combination?
There is command lines below that I'm using to make my combination, as
presented by Bocard in Numerical Ecology Analysis with R chapter 4 or 5.
with this code, it is possible to join PCA and Cluster however, without
differentiating the colors of each ecosystem.
#PCA
mydata.pca<-rda(mydata)
#Cluster
mydata.w <- hclust(dist(Sqchord.mydata), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
# Cut the dendrogram to yield 5 groups
gr <- cutree(mydata.w, k=5)
grl <- levels(factor(gr))
# Get the site scores, scaling 1
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
# Plot the sites with cluster symbols and colours (scaling 3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
abline(v=0, lty="dotted")
abline(h=0, lty="dotted")
for (i in 1:length(grl))
{ points(sit.sc1[gr==i,], pch=(14+i), cex=2.5, col=i+1)}
text(sit.sc1, row.names(Pre_euro_veg.1.all), cex=0.7, pos=3)
# Add legend interactively
legend(locator(1), paste("Cluster", c(1:length(grl))),
pch=14+c(1:length(grl)),
col=1+c(1:length(grl)), pt.cex=2)
Thank you for any help.
Jackson Rodrigues
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
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.
