limma: plotWithHighlights – R documentation

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plotWithHighlights

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

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)

limma

Linear Models for Microarray Data

v3.46.0

GPL (>=2)

Authors

Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

Initial release

2020-10-19