pRoloc (version 1.12.4)

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 codeplot2D. 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 coderownames(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)