highlightOnPlot {pRoloc} | R Documentation

## Highlight features of interest on a spatial proteomics plot

### Description

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.

### Usage

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

    highlightOnPlot3D(object, foi, labels, args = list(), radius = 0.1 * 3,
      ...)

### 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` or `text` (when `labels` is `TRUE`) when adding to `plot2D`, or `spheres3d` or `text3d` when adding the `plot3D`
`radius` | 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.

### Value

NULL; used for its side effects.

### Author(s)

Laurent Gatto

### 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)

    ## in 3 dimensions
    if (interactive()) {
      plot3D(tan2009r1, radius1 = 0.05)
      highlightOnPlot3D(tan2009r1, x, labels = TRUE)
      highlightOnPlot3D(tan2009r1, x)
    }

[Package pRoloc version 1.26.0 Index]