PCA.biplot: The Principal Component Analysis (PCA) biplot

In PLSbiplot1: The Partial Least Squares (PLS) Biplot

Description

Takes in a samples by variables data matrix and produces a PCA biplot.

Usage

PCA.biplot(D, method = NULL, ax.tickvec.D = NULL, ...)

Arguments

D	A samples by variables data matrix
method	the mod.PCA algorithm
ax.tickvec.D	tick marker length per axis in the PCA biplot
...	Other arguments. Currently ignored

Value

The PCA biplot of D with some parameters

Author(s)

Opeoluwa F. Oyedele and Sugnet Gardner-Lubbe

Examples

if(require(pls))
data(oliveoil, package="pls")
Dmat = as.matrix(oliveoil)  #(16x11) overall original data matrix
dimnames(Dmat) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
"S1","S2","S3","S4","S5","S6")),
paste(c("Acidity","Peroxide","K232","K270","DK","Yellow",
"Green","Brown","Glossy","Transp","Syrup")))
PCA.biplot(D=Dmat, method=mod.PCA, ax.tickvec.D=c(8,5,5,7,6,4,5,5,8,7,7))

Example output

Loading required package: pls

Attaching package: 'pls'

The following object is masked from 'package:stats':

    loadings

$overall.quality
[1] 0.99

$axis.pred
 Acidity Peroxide     K232     K270       DK   Yellow    Green    Brown 
   0.935    0.993    0.997    0.987    0.635    0.978    0.940    0.981 
  Glossy   Transp    Syrup 
   0.998    0.997    0.999 

$sample.pred
   G1    G2    G3    G4    G5    I1    I2    I3    I4    I5    S1    S2    S3 
0.946 0.981 0.988 0.962 1.206 1.084 1.029 0.877 0.960 0.953 0.980 0.974 1.068 
   S4    S5    S6 
0.994 0.974 0.950 

$D.hat
   Acidity Peroxide K232   K270        DK Yellow Green Brown Glossy Transp
G1   0.654    13.24 1.79 0.1436  0.000781   17.0 76.84  8.35   76.0   69.8
G2   0.402    13.92 1.78 0.1282 -0.000893   39.9 46.98 12.23   78.5   74.7
G3   0.380    11.06 1.56 0.1124 -0.001863   50.9 35.48  8.44   83.2   80.7
G4   0.543    13.02 1.75 0.1343 -0.000101   28.7 62.14  9.32   77.9   73.0
G5   0.466    12.12 1.66 0.1241 -0.000923   39.0 49.68  8.94   80.4   76.5
I1   0.291    19.34 2.15 0.1465 -0.000195   34.4 49.28 21.19   71.8   67.2
I2   0.290    13.97 1.76 0.1200 -0.001712   50.9 32.89 13.60   80.0   77.4
I3   0.396    16.23 1.95 0.1391 -0.000289   33.4 53.20 15.57   75.1   70.5
I4   0.256    13.52 1.71 0.1153 -0.002086   55.6 27.29 13.36   81.2   79.0
I5   0.111    20.48 2.19 0.1386 -0.001208   48.7 29.93 24.89   72.6   69.5
S1   0.180    10.79 1.50 0.0962 -0.003423   71.5  9.26 10.39   86.4   86.1
S2   0.221     9.24 1.39 0.0917 -0.003547   72.1  9.89  7.72   88.2   88.0
S3   0.238    12.32 1.62 0.1081 -0.002559   61.0 21.33 11.87   83.3   81.8
S4   0.175    12.03 1.59 0.1020 -0.003104   68.1 12.50 12.19   84.6   83.8
S5   0.194    10.19 1.46 0.0943 -0.003482   71.9  9.32  9.36   87.1   86.9
S6   0.193    10.54 1.48 0.0959 -0.003395   71.0 10.18  9.88   86.6   86.2
   Syrup
G1  49.3
G2  48.9
G3  46.5
G4  48.7
G5  47.7
I1  52.8
I2  48.5
I3  50.7
I4  48.0
I5  53.0
S1  45.5
S2  44.4
S3  46.9
S4  46.5
S5  45.0
S6  45.3

PLSbiplot1 documentation built on May 2, 2019, 9:41 a.m.