使用《Bioinformatics and Molecular Evolution》Table 2.2 (page 24)中的数据:
> aa
VOL BULK POLARITY PI HYD1 HYD2 SURFACE_AREA FRACT_AREA
A 67 11.50 0.00 6.00 1.8 1.6 113 0.74
R 148 14.28 52.00 10.76 -4.5 -12.3 241 0.64
N 96 12.28 3.38 5.41 -3.5 -4.8 158 0.63
D 91 11.68 49.70 2.77 -3.5 -9.2 151 0.62
C 86 13.46 1.48 5.05 2.5 2.0 140 0.91
Q 114 14.45 3.53 5.65 -3.5 -4.1 189 0.62
E 109 13.57 49.90 3.22 -3.5 -8.2 183 0.62
G 48 3.40 0.00 5.97 -0.4 1.0 85 0.72
H 118 13.69 51.60 7.59 -3.2 -3.0 194 0.78
I 124 21.40 0.13 6.02 4.5 3.1 182 0.88
L 124 21.40 0.13 5.98 3.8 2.8 180 0.85
K 135 15.71 49.50 9.74 -3.9 -8.8 211 0.52
M 124 16.25 1.43 5.74 1.9 3.4 204 0.85
F 135 19.80 0.35 5.48 2.8 3.7 218 0.88
P 90 17.43 1.58 6.30 -1.6 -0.2 143 0.64
S 73 9.47 1.67 5.68 -0.8 0.6 122 0.66
T 93 15.77 1.66 5.66 -0.7 1.2 146 0.70
W 163 21.67 2.10 5.89 -0.9 1.9 259 0.85
Y 141 18.03 1.61 5.66 -1.3 -0.7 229 0.76
V 105 21.57 0.13 5.96 4.2 2.6 160 0.85
> aa.pc=prcomp(aa, center=TRUE, scale.=TRUE)
> aa.pc
Standard deviations:
[1] 1.88954924 1.67729608 0.88574923 0.65278312 0.53130822 0.27233782 0.21394709
[8] 0.05808934
Rotation:
PC1 PC2 PC3 PC4 PC5
VOL 0.05790316 -0.58494270 0.1057571970 -0.09311996 0.1684497
BULK -0.22089815 -0.48085679 0.1685873871 -0.15647005 -0.6842181
POLARITY 0.44390146 -0.10372198 0.1432388489 0.73088587 -0.1747201
PI 0.18580066 -0.25244261 -0.9417631776 0.02722752 -0.0522075
HYD1 -0.49279466 -0.03284274 -0.1281013177 0.35033569 -0.3534423
HYD2 -0.50821923 0.03312719 -0.1292531953 -0.12776013 0.1837842
SURFACE_AREA 0.10045084 -0.56587879 0.1408585179 -0.10640314 0.3652725
FRACT_AREA -0.45283231 -0.17244828 0.0009997326 0.53059489 0.4220135
PC6 PC7 PC8
VOL -0.11705506 0.21351836 -0.739571539
BULK 0.25124136 -0.35181704 0.109655303
POLARITY 0.39252691 0.22974777 0.009653888
PI 0.04562347 -0.09136074 0.030622127
HYD1 -0.50083501 0.48686655 0.064292387
HYD2 0.70974650 0.41191312 -0.019940539
SURFACE_AREA -0.11107422 0.24097250 0.659316956
FRACT_AREA -0.01018472 -0.55201871 -0.027363410
> summary(aa.pc)
Importance of components:
PC1 PC2 PC3 PC4 PC5 PC6 PC7
Standard deviation 1.8895 1.6773 0.88575 0.65278 0.53131 0.27234 0.21395
Proportion of Variance 0.4463 0.3517 0.09807 0.05327 0.03529 0.00927 0.00572
Cumulative Proportion 0.4463 0.7980 0.89603 0.94930 0.98459 0.99386 0.99958
PC8
Standard deviation 0.05809
Proportion of Variance 0.00042
Cumulative Proportion 1.00000
PC1和PC2能够解释79.8%的variation。
