setwd("/home/duncan/Dropbox/Public/Analyses/matan")
a<-dir()
d<-read.csv(a[1])
d2<-read.csv(a[2])
library(reshape)
d1<-data.frame(id=1:186,d)
d1<-melt(d1,id=1)
library(ggplot2)


str(d1)
## 'data.frame':    3162 obs. of  3 variables:
##  $ id      : int  1 2 3 4 5 6 7 8 9 10 ...
##  $ variable: Factor w/ 17 levels "Mg","Si","K",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ value   : num  3141 1130 0 2361 1401 ...
g0<-ggplot(d1,aes(x=value))
g1<-g0 + geom_histogram(fill="grey",colour="black") + theme_bw()
g1+facet_wrap(~variable)

plot of chunk unnamed-chunk-2

g0<-ggplot(d1,aes(x=log10(value)))
g1<-g0 + geom_histogram(fill="grey",colour="black") + theme_bw()
g1+facet_wrap(~variable)

plot of chunk unnamed-chunk-2

g0<-ggplot(d1,aes(sample=log10(value)))
g1<-g0 +  stat_qq() + theme_bw()
g1+facet_wrap(~variable)

plot of chunk unnamed-chunk-2

library(GGally)
f<-function(x)log10(x+0.1)
d2<-f(d)
ggpairs(d2[,1:8])

plot of chunk unnamed-chunk-3

ggpairs(d2[,9:17])

plot of chunk unnamed-chunk-3

So some problems with the zeros. We can still use PCA

PCA

pca<-prcomp(d2,scale=TRUE,center=TRUE,retx=TRUE)
plot(pca)

plot of chunk unnamed-chunk-4

biplot(pca)

plot of chunk unnamed-chunk-4

pca
## Standard deviations:
##  [1] 2.5617 1.7606 1.3459 0.9725 0.9174 0.8688 0.7874 0.6981 0.6717 0.5763
## [11] 0.5440 0.5270 0.4086 0.3675 0.3200 0.2651 0.2126
## 
## Rotation:
##         PC1      PC2      PC3       PC4       PC5      PC6      PC7
## Mg -0.10902  0.39868 -0.03883  0.198026 -0.121227  0.50623 -0.42902
## Si -0.32056  0.22056  0.11034  0.058839 -0.139682  0.16548  0.02300
## K   0.07580  0.39811  0.26051  0.009638  0.101057  0.03472  0.28176
## Ca -0.26913  0.02609 -0.45587 -0.152006  0.052248  0.16873  0.02297
## P   0.13706  0.35216  0.16802  0.339847  0.331035 -0.14698  0.17924
## Fe -0.36454 -0.04480  0.11134 -0.017452 -0.100942 -0.17822  0.09934
## Ti -0.36002 -0.03413  0.16952  0.024166 -0.181312 -0.01580  0.14380
## Mn -0.28004 -0.05267 -0.09905  0.509381  0.095089  0.13358 -0.10929
## Al -0.31889  0.15965 -0.06175 -0.227934 -0.236034  0.15610  0.27242
## Sr -0.16792  0.06104 -0.46818 -0.078047  0.565975  0.10908  0.16932
## S   0.01812  0.37556 -0.31120  0.160440 -0.409367 -0.32564 -0.07414
## Cl  0.07646  0.38410 -0.31746  0.022835 -0.061607 -0.42985  0.16508
## V  -0.30339  0.10946  0.19456 -0.419078  0.052643 -0.09757  0.16099
## Cr -0.27230 -0.03207  0.10116 -0.039922  0.006731 -0.44515 -0.53435
## Zn -0.09342  0.33976  0.25228 -0.277453  0.430573 -0.05863 -0.36920
## Zr -0.26572 -0.08927  0.25226  0.442813  0.108200 -0.07485  0.26533
## Ba -0.25667 -0.22151 -0.18830  0.153885  0.209349 -0.26723 -0.08425
##         PC8      PC9      PC10       PC11      PC12     PC13     PC14
## Mg  0.03363 -0.01302 -0.047001  0.3584678 -0.024633  0.33272  0.28227
## Si -0.04361 -0.19707 -0.020542  0.1102417  0.103583 -0.10990 -0.74198
## K   0.71863  0.17754 -0.002162  0.0664442  0.130382 -0.30262  0.11926
## Ca -0.10677 -0.02310  0.181907 -0.0152396 -0.137041 -0.53669  0.36062
## P  -0.19794 -0.46288  0.454656 -0.0999960 -0.204357  0.07943  0.09059
## Fe  0.05062  0.00157 -0.015992 -0.0561773  0.009588  0.07103  0.04362
## Ti -0.04814  0.03748 -0.058978  0.0545765  0.001466 -0.05425  0.10198
## Mn  0.19280  0.21437 -0.136957 -0.5412576 -0.421147 -0.01630 -0.11048
## Al -0.08795 -0.17232  0.242437  0.0036855 -0.082615 -0.08286 -0.01660
## Sr  0.11202 -0.20500 -0.255564 -0.0781447  0.394072  0.23281 -0.08596
## S  -0.06127  0.20755  0.207191 -0.3500172  0.471053  0.11513  0.04409
## Cl -0.10376  0.08216 -0.444263  0.3306388 -0.442530 -0.01383 -0.08331
## V   0.04767  0.09789 -0.005585 -0.1935435 -0.201403  0.54638  0.19159
## Cr  0.25442 -0.49872 -0.150308 -0.0003119  0.061850 -0.15778  0.14448
## Zn -0.35031  0.41191  0.024918 -0.1056246  0.046923 -0.23134 -0.11508
## Zr -0.34779  0.11615 -0.261737  0.1981394  0.325342 -0.08687  0.28695
## Ba  0.20598  0.32297  0.528141  0.4688048 -0.037202  0.15506 -0.15195
##         PC15     PC16     PC17
## Mg -0.065060  0.06381 -0.04613
## Si -0.028290 -0.36457 -0.15863
## K   0.030940 -0.01951 -0.02216
## Ca -0.127344 -0.35982 -0.19088
## P  -0.147204 -0.03403  0.03013
## Fe -0.535476  0.44048 -0.55390
## Ti -0.462932 -0.04853  0.73886
## Mn  0.137921  0.06622  0.05102
## Al  0.505208  0.52814  0.13570
## Sr -0.073599  0.12651  0.13268
## S   0.012500 -0.08019  0.03121
## Cl  0.005413  0.04463  0.01752
## V   0.159940 -0.42932 -0.09613
## Cr  0.198765 -0.01779  0.06169
## Zn -0.013952  0.18012  0.06559
## Zr  0.321287 -0.10330 -0.14884
## Ba  0.081942 -0.01178  0.05250

So two quite orthoganal axes, the first capturing silicon, barium etc and the second magnesium zinc etc (see rotated loadings). This is useful for further analysis.