plotWithHighlights {limma} | R Documentation

## Scatterplot With Highlighting of Special Points

### Description

Creates scatterplot, with optional size and color coding for points of special interest. This is the engine for `plotMD` and `plotMA`.

### Usage

    plotWithHighlights(x, y, status = NULL, values = NULL,
                       hl.pch = 16, hl.col = NULL, hl.cex = 1, legend = "topright",
                       bg.pch = 16, bg.col = "black", bg.cex = 0.3,
                       pch = NULL, col = NULL, cex = NULL, ...)

### Arguments

`x` | numeric vector.
`y` | numeric vector of same length as `x`.
`status` | character vector giving the control status of each point, of same length as `x` and `y`, or else a `TestResults` object with one column and number of rows matching the length of `x`. If `NULL`, then all points are plotted in the background color, symbol and size.
`values` | character vector giving values of `status` to be highlighted on the plot. Set automatically if `status` contains `TestResults`. Defaults to unique values of `status` in decreasing order of frequency, with the most frequent value set as the background value. Ignored if there is no `status` vector.
`hl.pch` | vector of plotting characters for highlighted points, either of unit length or of same length as `values`. Ignored is there is no `status` vector.
`hl.col` | vector of colors for highlighted points, either of unit length or of same length as `values`. Set automatically if `status` contains `TestResults`. Defaults to `1+1:length(values)`. Ignored if there is no `status` vector.
`hl.cex` | numeric vector of plot symbol expansions for highlighted points, either of unit length or of same length as `values`. Ignored if there is no `status` vector.
`legend` | character string giving position to place legend. See `legend` for possible values. Can also be logical, with `FALSE` meaning no legend. Ignored if there is no `status` vector.
`bg.pch` | plotting character for background (non-highlighted) points.
`bg.col` | color for background (non-highlighted) points.
`bg.cex` | plot symbol expansion for background (non-highlighted) points.
`pch` | synonym for `hl.pch` allowed for backward compatibility.
`col` | synonym for `hl.col` allowed for backward compatibility.
`cex` | synonym for `hl.cex` allowed for backward compatibility.
`...` | other arguments are passed to `plot`.

### Details

This function produces a scatterplot in which the highlighted points are, by default, larger and colored compared to background points.

The `status` vector establishes the status of each point and `values` indicates which values of `status` should be highlighted. If `values=NULL`, then the most common value of `status` is assumed to correspond to background points and all other values are highlighted.

The arguments `hl.pch`, `hl.col` and `hl.cex` give graphics settings for highlighted points. By default, highlighted points are larger than background points and a different color is used for each distinct highlighted value.

The arguments `bg.pch`, `bg.col` and `bg.cex` give the graphics settings for non-highlighted (background) points. The same settings are used for all background points.

The arguments `values`, `pch`, `col` and `cex` can be included as attributes to `status` instead of being passed as arguments to `plotWithHighlights`. This is for compatibility with `controlStatus`.

See `points` for possible values for the graphics parameters.

### Value

A plot is created on the current graphics device.

### Author(s)

Gordon Smyth

### References

Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47. http://nar.oxfordjournals.org/content/43/7/e47

### See Also

`plotMD`, `plotMA`, `mdplot`

An overview of diagnostic plots available in LIMMA is given in 09.Diagnostics.

### Examples

    x <- runif(1000, min=4, max=16)
    status <- rep(c(0,-1,1), c(950,40,10))
    y <- status + rnorm(1000, sd=0.2)
    plotWithHighlights(x, y, status=status)

[Package limma version 3.50.3 Index]