R/plotting.R
, R/plotting3.R
highlightOnPlot.Rd
Highlights a set of features of interest given as a
FeaturesOfInterest
instance on a PCA plot produced by
plot2D
or plot3D
. If none of the features of interest
are found in the MSnset
's featureNames
, an warning
is thrown.
The main dataset described as an MSnSet
or a
matrix
with the coordinates of the features on the PCA
plot produced (and invisibly returned) by plot2D
.
An instance of FeaturesOfInterest
,
or, alternatively, a character
of feautre names.
A character
of length 1 with a feature
variable name to be used to label the features of
interest. This is only valid if object
is an
MSnSet
. Alternatively, if TRUE
, then
featureNames(object)
(or rownames(object)
, if
object
is a matrix
) are used. Default is
missing, which does not add any label.s
A named list of arguments to be passed to
plot2D
if the PCA coordinates are to be
calculated. Ignored if the PCA coordinates are passed
directly, i.e. object
is a matrix
.
Additional parameters passed to points
or
text
(when labels
is TRUE
) when adding to
plot2D
, or spheres3d
or text3d
when
adding the plot3D
Radius of the spheres to be added to the
visualisation produced by plot3D
. Default is 0.3 (i.e
plot3D
's radius1
* 3), to emphasise the features
with regard to uknown (radius1 = 0.1
) and marker
(radius1
* 2) features.
NULL; used for its side effects.
library("pRolocdata")
data("tan2009r1")
x <- FeaturesOfInterest(description = "A test set of features of interest",
fnames = featureNames(tan2009r1)[1:10],
object = tan2009r1)
## using FeaturesOfInterest or feature names
par(mfrow = c(2, 1))
plot2D(tan2009r1)
highlightOnPlot(tan2009r1, x)
plot2D(tan2009r1)
highlightOnPlot(tan2009r1, featureNames(tan2009r1)[1:10])
.pca <- plot2D(tan2009r1)
head(.pca)
#> PC1 (58.53%) PC2 (29.96%)
#> P20353 0.2103374 1.6959266
#> P53501 -0.4940607 1.6207386
#> Q7KU78 -1.1794311 -0.7242185
#> P04412 0.6128549 0.3944441
#> Q7KJ73 0.1866756 -0.3007028
#> Q7JZN0 2.0228016 -1.3087061
highlightOnPlot(.pca, x, col = "red")
highlightOnPlot(tan2009r1, x, col = "red", cex = 1.5)
highlightOnPlot(tan2009r1, x, labels = TRUE)
.pca <- plot2D(tan2009r1, dims = c(1, 3))
highlightOnPlot(.pca, x, pch = "+", dims = c(1, 3))
#> Warning: "dims" is not a graphical parameter
highlightOnPlot(tan2009r1, x, args = list(dims = c(1, 3)))
.pca2 <- plot2D(tan2009r1, mirrorX = TRUE, dims = c(1, 3))
## previous pca matrix, need to mirror X axis
highlightOnPlot(.pca, x, pch = "+", args = list(mirrorX = TRUE))
## new pca matrix, with X mirrors (and 1st and 3rd PCs)
highlightOnPlot(.pca2, x, col = "red")
plot2D(tan2009r1)
highlightOnPlot(tan2009r1, x)
highlightOnPlot(tan2009r1, x, labels = TRUE, pos = 3)
highlightOnPlot(tan2009r1, x, labels = "Flybase.Symbol", pos = 1)
## in 3 dimensions
if (interactive()) {
plot3D(tan2009r1, radius1 = 0.05)
highlightOnPlot3D(tan2009r1, x, labels = TRUE)
highlightOnPlot3D(tan2009r1, x)
}