PLS.biplot: The Partial Least Squares (PLS) biplot

Description Usage Arguments Value Author(s) Examples

View source: R/AllFunctions.R

Description

Takes in a set of predictor variables and a set of response variables and produces a PLS biplot.

Usage

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PLS.biplot(X, Y, algorithm = NULL, ax.tickvec.X = NULL,
  ax.tickvec.Y = NULL, ...)

Arguments

X

A (NxP) predictor matrix

Y

A (NxM) response matrix

algorithm

Any of the PLS algorithms ("mod.NIPALS", "mod.KernelPLS_R", "mod.KernelPLS_L", "mod.SIMPLS")

ax.tickvec.X

tick marker length for each X-variable axis in the PLS biplot

ax.tickvec.Y

tick marker length for each Y-variable axis in the PLS biplot

...

Other arguments. Currently ignored

Value

The PLS biplot of D=[X Y] with some parameters

Author(s)

Opeoluwa F. Oyedele and Sugnet Gardner-Lubbe

Examples

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if(require(pls))
data(oliveoil, package="pls")
X = as.matrix(oliveoil$chemical, ncol=5)
dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
"S1","S2","S3","S4","S5","S6")),
paste(c("Acidity","Peroxide","K232","K270","DK")))
Y = as.matrix(oliveoil$sensory, ncol=6)
dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
"S1","S2","S3","S4","S5","S6")),
paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
#SIMPLS biplot
PLS.biplot(X, Y, algorithm=mod.SIMPLS, ax.tickvec.X=c(8,5,5,5,5), ax.tickvec.Y=c(5,8,5,6,9,8))
#Kernel PLS biplot
PLS.biplot(X, Y, algorithm=mod.KernelPLS_R, ax.tickvec.X=c(3,3,4,5,2), ax.tickvec.Y=c(3,3,5,6,7,6))

Example output

Loading required package: pls

Attaching package: 'pls'

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

    loadings

$overall.quality
[1] 0.972

$axis.pred
 Acidity Peroxide     K232     K270       DK   Yellow    Green    Brown 
   0.988    0.995    0.999    0.989    0.753    0.934    0.819    0.963 
  Glossy   Transp    Syrup 
   0.997    0.994    0.998 

$D.hat
   Acidity Peroxide K232   K270        DK Yellow Green Brown Glossy Transp
G1   0.756    13.49 1.80 0.1487  0.001917   26.7  65.1  9.45   76.9   71.5
G2   0.179    12.88 1.66 0.1075 -0.002936   58.9  23.2 12.80   82.4   80.7
G3   0.229    11.46 1.56 0.1035 -0.002986   60.6  22.4 10.55   83.9   82.2
G4   0.629    13.68 1.80 0.1413  0.000945   32.9  56.8 10.61   77.7   73.0
G5   0.511    10.85 1.56 0.1191 -0.000901   47.5  40.2  7.71   82.4   79.1
I1   0.299    18.80 2.12 0.1454 -0.000111   35.2  49.1 19.79   73.6   69.7
I2   0.270    15.37 1.86 0.1261 -0.001422   46.8  36.9 15.45   78.3   75.5
I3   0.309    17.01 1.99 0.1371 -0.000588   39.9  44.5 17.34   75.8   72.3
I4   0.322    14.47 1.80 0.1250 -0.001289   46.8  37.8 13.87   79.1   76.2
I5   0.156    20.13 2.20 0.1428 -0.000844   38.8  43.2 22.59   72.9   69.6
S1   0.186    11.40 1.55 0.1004 -0.003354   63.0  19.2 10.78   84.3   82.9
S2   0.261    10.16 1.47 0.0991 -0.003132   62.7  20.8  8.59   85.3   83.8
S3   0.250    11.53 1.57 0.1053 -0.002790   59.2  24.1 10.48   83.6   81.8
S4   0.171    11.28 1.53 0.0988 -0.003514   64.2  17.8 10.73   84.6   83.3
S5   0.224     9.42 1.40 0.0929 -0.003666   66.8  16.0  7.88   86.6   85.4
S6   0.239    10.11 1.46 0.0973 -0.003332   64.0  19.1  8.69   85.6   84.2
   Syrup
G1  48.7
G2  47.5
G3  46.6
G4  48.7
G5  46.6
I1  51.8
I2  49.4
I3  50.6
I4  48.8
I5  52.6
S1  46.5
S2  45.8
S3  46.7
S4  46.4
S5  45.2
S6  45.7

$Bmat
         Yellow Green   Brown Glossy Transp  Syrup
Acidity  -1.175 1.343 -1.1120 -0.357 -0.604 -0.119
Peroxide -0.921 0.675  2.3788 -1.638 -1.364  1.862
K232     -1.169 0.977  1.9839 -1.646 -1.448  1.741
K270     -1.365 1.301  0.9420 -1.348 -1.314  1.206
DK       -1.042 1.071  0.0458 -0.748 -0.818  0.515

$overall.quality
[1] 0.972

$axis.pred
 Acidity Peroxide     K232     K270       DK   Yellow    Green    Brown 
   0.988    0.995    0.999    0.989    0.754    0.934    0.819    0.963 
  Glossy   Transp    Syrup 
   0.997    0.994    0.998 

$D.hat
   Acidity Peroxide K232   K270        DK Yellow Green Brown Glossy Transp
G1   0.757    13.49 1.80 0.1486  0.001934   26.8  65.1  9.43   76.9   71.5
G2   0.179    12.89 1.66 0.1075 -0.002943   58.9  23.2 12.81   82.4   80.7
G3   0.228    11.47 1.56 0.1035 -0.002992   60.6  22.4 10.56   83.9   82.2
G4   0.627    13.69 1.80 0.1412  0.000948   33.0  56.7 10.63   77.7   73.0
G5   0.510    10.86 1.56 0.1190 -0.000892   47.5  40.1  7.71   82.4   79.1
I1   0.299    18.79 2.12 0.1455 -0.000113   35.1  49.2 19.78   73.6   69.7
I2   0.271    15.37 1.86 0.1262 -0.001421   46.8  37.0 15.44   78.3   75.5
I3   0.310    17.01 1.99 0.1371 -0.000587   39.9  44.6 17.33   75.8   72.3
I4   0.322    14.46 1.80 0.1250 -0.001286   46.8  37.8 13.86   79.1   76.2
I5   0.155    20.13 2.20 0.1429 -0.000860   38.7  43.2 22.61   72.9   69.6
S1   0.185    11.40 1.55 0.1004 -0.003358   63.0  19.2 10.79   84.3   82.9
S2   0.262    10.16 1.47 0.0991 -0.003129   62.7  20.8  8.58   85.3   83.8
S3   0.251    11.52 1.57 0.1053 -0.002788   59.2  24.1 10.47   83.6   81.8
S4   0.171    11.27 1.53 0.0988 -0.003515   64.1  17.8 10.72   84.6   83.3
S5   0.224     9.42 1.40 0.0929 -0.003663   66.8  16.0  7.87   86.6   85.4
S6   0.238    10.11 1.46 0.0973 -0.003333   64.0  19.0  8.69   85.6   84.2
   Syrup
G1  48.7
G2  47.5
G3  46.6
G4  48.7
G5  46.6
I1  51.8
I2  49.4
I3  50.6
I4  48.8
I5  52.6
S1  46.5
S2  45.8
S3  46.7
S4  46.4
S5  45.2
S6  45.7

$Bmat
         Yellow  Green  Brown  Glossy  Transp   Syrup
Acidity  -0.233 0.2774 -0.313 -0.0334 -0.0955 -0.0784
Peroxide -0.105 0.0562  0.453 -0.2622 -0.2050  0.3213
K232     -0.159 0.1228  0.352 -0.2576 -0.2188  0.2859
K270     -0.217 0.2111  0.117 -0.2012 -0.2004  0.1723
DK       -0.183 0.1965 -0.059 -0.1041 -0.1261  0.0506

PLSbiplot1 documentation built on May 30, 2017, 12:52 a.m.