sopls_plots {multiblock} | R Documentation |
Scores, loadings and plots for sopls objects
Description
Extraction of scores
and loadings
and adaptation of scoreplot
,
loadingplot
and biplot
from package pls
for sopls
objects.
Usage
## S3 method for class 'sopls'
loadings(object, ncomp = "all", block = 1, y = FALSE, ...)
## S3 method for class 'sopls'
scores(object, ncomp = "all", block = 1, y = FALSE, ...)
## S3 method for class 'sopls'
scoreplot(
object,
comps = 1:2,
ncomp = NULL,
block = 1,
labels,
identify = FALSE,
type = "p",
xlab,
ylab,
...
)
## S3 method for class 'sopls'
loadingplot(
object,
comps = 1:2,
ncomp = NULL,
block = 1,
scatter = TRUE,
labels,
identify = FALSE,
type,
lty,
lwd = NULL,
pch,
cex = NULL,
col,
legendpos,
xlab,
ylab,
pretty.xlabels = TRUE,
xlim,
...
)
## S3 method for class 'sopls'
corrplot(
object,
comps = 1:2,
ncomp = NULL,
block = 1,
labels = TRUE,
col = 1:5,
plotx = TRUE,
ploty = TRUE,
...
)
## S3 method for class 'sopls'
biplot(
x,
comps = 1:2,
ncomp = "all",
block = 1,
which = c("x", "y", "scores", "loadings"),
var.axes = FALSE,
xlabs,
ylabs,
main,
...
)
Arguments
object |
|
ncomp |
|
block |
|
y |
|
... |
further arguments sent to the underlying plot function(s) |
comps |
|
labels |
|
identify |
|
type |
|
xlab |
|
ylab |
|
scatter |
|
lty |
Vector of line type specifications (see |
lwd |
|
pch |
Vector of point specifications (see |
cex |
|
col |
|
legendpos |
|
pretty.xlabels |
|
xlim |
|
plotx |
|
ploty |
|
x |
|
which |
|
var.axes |
|
xlabs |
|
ylabs |
|
main |
|
Details
If comps
is supplied as a list
for scoreplot
, it is assumed that its elements refer to each of the
blocks up to block number block
. For instance comps = list(1, 0, 1:2)
will select 1 component from the first
block, no components from the second block and the first two components from the last block. This must be
matched by ncomp
, specifying how many components were selected before block number block
.
See Also
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 are found in sopls_results
.
#' @return The score and loading functions return scores and loadings, while plot functions have no return (except use of 'identify').
Examples
data(potato)
so <- sopls(Sensory ~ Chemical + Compression + NIRraw, data=potato, ncomp=c(5,5,5))
# Loadings
loadings(so, ncomp=c(3), block=2)[, 1:3]
# Scores
scores(so, block=1)[, 1:4]
# Default plot from first block
scoreplot(so)
# Second block with names
scoreplot(so, ncomp=c(3), block=2, labels="names")
# Scatterplot matrix
scoreplot(so, ncomp=c(3,2), block=3, comps=1:3)
# Combination of blocks (see Details)
scoreplot(so, ncomp=c(3,2), block=3, comps=list(1,0,1))
# Default plot from first block
loadingplot(so, scatter=TRUE)
# Second block with names
loadingplot(so, ncomp=c(3), block=2, labels="names", scatter=TRUE)
# Scatterplot matrix
loadingplot(so, ncomp=c(3,2), block=3, comps=1:3, scatter=TRUE)
# Correlation loadings
corrplot(so, block=2, ncomp=1)
# Default plot from first block
biplot(so)