limma (version 3.28.14)

plotWithHighlights: Scatterplot With Highlighting of Special Points


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


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


numeric vector.
numeric vector.
character vector giving the control status of each point, of same length as x and y. If NULL, then all points are plotted in the background color, symbol and size.
character vector giving values of status to be highlighted on the plot. 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.
vector of plotting characters for highlighted points, either of unit length or of same length as values. Ignored is there is no status vector.
vector of colors for highlighted points, either of unit length or of same length as values. Defaults to 1+1:length(values). Ignored if there is no status vector.
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.
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.
plotting character for background (non-highlighted) points.
color for background (non-highlighted) points.
plot symbol expansion for background (non-highlighted) points.
synonym for hl.pch allowed for backward compatibility.
synonym for hl.col allowed for backward compatibility.
synonym for hl.cex allowed for backward compatibility.
other arguments are passed to plot.



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.


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.

See Also

plotMD, plotMA, mdplot

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


Run this code
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)

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