Hello can anyone help,
I have been running the following script to obtain a PCA plot but the end result
is rather disappointing as the points are very very small and there are no
titles etc
geochemdata<-read.csv(file.choose(),header=TRUE)
names(geochemdata)
library(vegan)
bstick<-function(n, tot.var=1) rev(cumsum(tot.var/n:1)/n)
geopca<-rda(geochemdata, scale=TRUE)
geopca
geopca$CA$eig/geopca$tot.chi
summary(geopca, scaling=2)
apply(scores(geopca, choices=1.6, display= "species"),
+ 2,function(x) x/sd(x))
plot(geopca$CA$eig, type= "o", col= "red", xlab= "PCA
Axis",
ylab= "Variance", main= "Scree plot for the PCA of the Geochem
Data")
bstick.env<- bstick(19, tot.var=19) #must change number based on number in
bstick model
bstick.env
geopca
plot(bstick.env, type="o", lty="dotted",
ylim=range(bstick.env,
geopca$CA$eig), xlab="PCA Axis", ylab="Inertia",
main="Geochemical ITRAX Data: Bstick")
points(geopca$CA$eig, type="o", col="red")
plot(geopca, scaling=2)
env.sc<- scores(geopca)$species
plot(geopca, scaling=2)
arrows(0, 0, env.sc[,1]*0.85, env.sc[,2]*0.85,
col="red", length=0.05)
Does anyone know a more suitable code? I have also tried
eochemdata<-read.csv(file.choose(),header=TRUE)
names(geochemdata)
fit <- princomp(geochemdata, cor=TRUE)
summary(fit) # print variance accounted for
loadings(fit) # pc loadings
plot(fit) # scree plot
fit$scores # the principal components
write.csv(fit$scores, file="trial.csv") # export output of PCA
which does work but again I cannot seem to adjust the output. All the titles
become squashed/un-readable and the points are in text format rather than appear
as mere dots. Is there code to allow the user to move things about as they so
wish and set their own style? I have used all the online suggestions but they
keep coming back with error comments.
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