highlightOnPlot {pRoloc} | R Documentation |
Highlights a set of features of interest given as a
FeaturesOfInterest
instance on a PCA plot produced by
codeplot2D or plot3D
. If none of the features of interest
are found in the MSnset
's featureNames
, an warning
is thrown.
highlightOnPlot(object, foi, labels, args = list(), ...) highlightOnPlot3D(object, foi, labels, args = list(), radius = 0.1 * 3, ...)
object |
The main dataset described as an |
foi |
An instance of |
labels |
A |
args |
A named list of arguments to be passed to
|
... |
Additional parameters passed to |
radius |
Radius of the spheres to be added to the
visualisation produced by |
NULL; used for its side effects.
Laurent Gatto
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) 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)) 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 plot3D(tan2009r1, radius1 = 0.05) highlightOnPlot3D(tan2009r1, x, labels = TRUE) highlightOnPlot3D(tan2009r1, x)