Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/plotWithHighlights.R
Creates scatterplot, with optional size and color coding for points of special interest.
This is the engine for plotMD
and plotMA
.
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x |
numeric vector. |
y |
numeric vector of same length as |
status |
character vector giving the control status of each point, of same length as |
values |
character vector giving values of |
hl.pch |
vector of plotting characters for highlighted points, either of unit length or of same length as |
hl.col |
vector of colors for highlighted points, either of unit length or of same length as |
hl.cex |
numeric vector of plot symbol expansions for highlighted points, either of unit length or of same length as |
legend |
character string giving position to place legend.
See |
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 |
col |
synonym for |
cex |
synonym for |
... |
other arguments are passed to |
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.
A plot is created on the current graphics device.
Gordon Smyth
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
An overview of diagnostic plots available in LIMMA is given in 09.Diagnostics.
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