ASCA.PlotLoadings: Loadings plot for a specific factor/interaction of the ASCA

In MetStaT: Statistical metabolomics tools

Description

Allows the user to plot a single loadings plot for one factor or interaction (or for the SVD on the original data)

Usage

ASCA.PlotLoadings(asca, ee= "", pcs = c(1,2))

Arguments

asca	Results of a performed ASCA analysis
ee	Which factor or interaction to use (eg. "1", or "12", or leave empty to use the original data)
pcs	Which PCs (Principal Components) to use for plotting (eg. c1,2)

Value

Only the plot is returned.

Note

Output of ASCA.Calculate is required.

Author(s)

Tim Dorscheidt

Examples

##Plot selected loadings after doing PerformAsca
## use the data matrix, ASCAX, and an experimental design matrix, ASCAF.
data(ASCAdata)
ASCA <- ASCA.Calculate(ASCAX, ASCAF, equation.elements = "1,2,12", scaling = TRUE)

## plot the loadings of the first two principal components of the first factor
ASCA.PlotLoadings(ASCA, ee = "1", pcs="1,2")

Example output

Loading required package: MASS
Loading required package: abind
Loading required package: pls

Attaching package: 'pls'

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

    loadings

Variance explained per principal component (if >1%):
Whole data set 	PC1: 52.84%   PC2: 22.89%   PC3: 18.92%   PC4: 5.34%    
Factor 1     	PC1: 100.00%  PC2:  NA%     PC3:  NA%     PC4:  NA%     
Factor 2     	PC1: 91.34%   PC2: 8.66%    PC3:  NA%     PC4:  NA%     
Interaction 12	PC1: 88.72%   PC2: 11.28%   PC3:  NA%     PC4:  NA%     

Percentage each effect contributes to the total sum of squares:
Overall means  	0.96%
Factor 1     	0.00%
Factor 2     	0.00%
Interaction 12	0.00%
Residuals      	0.00%

Percentage each effect contributes to the sum of squares of the centered data:
Factor 1     	0.00%
Factor 2     	0.00%
Interaction 12	0.00%
Residuals      	0.00%

MetStaT documentation built on May 2, 2019, 1:45 p.m.