negation {ordr} | R Documentation |
Negation of ordination axes
Description
Negate the coordinates of a subset of ordination axes in both row and column singular vectors.
Usage
get_negation(x)
revert_negation(x)
negate_ord(x, negation = NULL)
negate_to_first_orthant(x, .matrix)
Arguments
x |
A tbl_ord. |
negation |
Integer vector of coordinates to negate. |
.matrix |
A character string partially matched (lowercase) to several
indicators for one or both matrices in a matrix decomposition used for
ordination. The standard values are |
Details
For purposes of comparison and visualization, it can be useful to negate the
(already artificial) coordinates of an ordination, either by fixed criteria
or to better align with another basis (matrix) of coordinates. negate_ord()
allows the user to negate specified coordinates of an ordination.
get_negation()
accesses the negations of an ordination, an integer vector
of 1
s and -1
s stored as a "negate"
attribute.
Value
negate_ord()
and negate_to_first_orthant()
return a tbl_ord with
certain axes negated but the wrapped model unchanged. get_negation()
returns the current negations. revert_negation()
returns the tbl_ord
without any manual negations.
A tbl_ord; the wrapped model is unchanged.
Examples
(pca <- ordinate(iris, cols = 1:4, prcomp))
ggbiplot(pca) + geom_rows_point() + geom_cols_vector()
# manually negate second coordinate
(pca_neg <- negate_ord(pca, 2))
ggbiplot(pca_neg) + geom_rows_point() + geom_cols_vector()
# NB: 'prcomp' method takes precedence; negations are part of the wrapper
biplot(pca)
biplot(pca_neg)
# negate to the first orthant
(pca_orth <- negate_to_first_orthant(pca, "v"))
get_negation(pca_orth)