pcagca | R Documentation |
PCA-GCA is a methods which aims at estimating subspaces of common, local and distinct variation from two or more blocks.
pcagca(
X,
commons = 2,
auto = TRUE,
auto.par = list(explVarLim = 40, rLim = 0.8),
manual.par = list(ncomp = 0, ncommon = 0),
tol = 10^-12
)
X |
|
commons |
|
auto |
|
auto.par |
|
manual.par |
|
tol |
|
The name PCA-GCA comes from the process of first applying PCA to each block, then using GCA to estimate local and common components, and finally orthogonalising the block-wise scores on the local/common ones and re-estimating these to obtain distinct components. The procedure is highly similar to the supervised method PO-PLS, where the PCA steps are exchanged with PLS.
multiblock
object including relevant scores and loadings. Relevant plotting functions: multiblock_plots
and result functions: multiblock_results
. Distinct components are marked as 'D(x), Comp c' for block x and component c
while local and common components are marked as "C(x1, x2), Comp c", where x1 and x2 (and more) are block numbers.
Smilde, A., Måge, I., Naes, T., Hankemeier, T.,Lips, M., Kiers, H., Acar, E., and Bro, R.(2017). Common and distinct components in data fusion. Journal of Chemometrics, 31(7), e2900.
Overviews of available methods, multiblock
, and methods organised by main structure: basic
, unsupervised
, asca
, supervised
and complex
.
Common functions for computation and extraction of results and plotting are found in multiblock_results
and multiblock_plots
, respectively.
data(potato)
potList <- as.list(potato[c(1,2,9)])
pot.pcagca <- pcagca(potList)
# Show origin and type of all components
lapply(pot.pcagca$blockScores,colnames)
# Basic multiblock plot
plot(scores(pot.pcagca, block=2), comps=1, labels="names")
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