pRoloc (version 1.12.3)

highlightOnPlot: Highlight features of interest on a plot2D figure

Description

Highlights a set of features of interest given as a FeaturesOfInterest instance on a PCA plot produced by code{plot2D}. If none of the features of interest are found in the MSnset's featureNames, an warning is thrown.

Usage

highlightOnPlot(object, foi, labels, args = list(), ...)

Arguments

object

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.

foi

An instance of FeaturesOfInterest, or, alternatively, a character of feautre names.

labels

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 code{rownames(object)}, if object is a matrix) are used. Default is missing, which does not add any label.s

args

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.

Value

• NULL; used for its side effects.

Examples

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)