[R] Spider diagrams

[Vojtech Janousek]

Dear Mark,
A friend of mine, who is on r-help disscusion group has forwarded me your 
querry regarding the spiderplots.

I am very much using R for geochemical calculations (mainly WR geochemistry 
of igneous rocks, plus radiogenic isotopes). OC I did need to solve the 
problem with spiderdiagrams and here are fragments of my code. I trust they 
will be of help:

# normalization (A,B)
# Normalizes data for a spiderdiagram
#
# Parameters:
#   sample analyses [A]
#   normalizing values [B]
#
normalization<-function(A,B){
         C<-matrix(rep(NA,nrow(A)*length(B)),ncol=length(B))
         for (i in 1:nrow(A)){
             C[i,]<-A[i,]/B
         }
         dimnames(C)<-dimnames(A)
         return(C)
     }


# spiderplot (A,B,model,ymin,ymax,add)
# Plots spiderdiagram
#
# Parameters:
#   normalized values [A]
#   normalizing values [B]
#   range of the diagram [ymin, ymax]
#   shall be the patterns unbroken even for missing values (join)

spiderplot<-function(A,B,ymin,ymax,join=T){
             if (ymin<=0) {ymin<-min(A,na.rm=TRUE)/10}
             if (ymax<=ymin) {ymax<-10*max(A,na.rm=TRUE)}
         windows(width = 8, height = 6.5, pointsize = 12)
         plot(A[1,],pch=1,xlab="",type="n",log="y",ylim=c(ymin,ymax),axes=FALSE,ylab="")
         axis(1, 1:length(B),labels=colnames(A))
         axis(2,)

         for (i in 1:nrow(A)){
                 points(A[i,],pch=i)
                 tempy<-A[i,][!is.na(A[i,])]
                 tempx<-(1:length(B))[!is.na(A[i,])]
                 if (join){
                         lines(tempx,tempy)}
                       else{
                         lines(1:length(B),A[i,])}
         }
}


#X is a numeric data matrix with data you need to normalize, samples in 
rows, elements in columns
# chondrit is a numeric vector with the normalizing values

Y<-normalization(X,chondrit)
spiderplot(Y,chondrit,1,1000)



My test data:
X:
         La    Ce   Pr    Nd Pm   Sm   Eu   Gd   Tb   Dy   Ho   Er   Tm   Yb
Sa-3 47.44 96.08   NA 45.15 NA 7.98 1.82   NA   NA 5.22 1.13 2.72   NA 2.95
Sa-4 21.67 71.78 6.94 29.71 NA 6.24 1.50 6.09 0.92 5.80 1.03 2.80 0.43 2.88
Sa-7 20.76 42.02 4.96 17.44 NA 3.76 1.77 3.76 0.56 2.70 0.56 1.64 0.24 1.52
        Lu
Sa-3 0.29
Sa-4 0.43
Sa-7 0.25


chondrit (REE in chondrites according to Boynton 1984)
     La     Ce     Pr     Nd     Pm     Sm     Eu     Gd     Tb     Dy     Ho
0.3100 0.8080 0.1220 0.6000 1.0000 0.1950 0.0735 0.2590 0.0474 0.3220 0.0718
     Er     Tm     Yb     Lu
0.2100 0.0324 0.2090 0.0322


I trust this will work for you. Please send any comments to my private 
email address since I am not on this discussion group (yet?).

                         Best regards,
                                                 Vojtech



                                               dr. Vojtech Janousek
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