plot.confband.points {sma}R Documentation

Highlights a Set of Points on the Current M vs A Plot

Description

This function highlights a prespecified proportion of extreme points on the M vs A plots.

Usage

plot.confband.points(A, M, crit1=0.025, crit2=crit1, nclass=10, ...)

Arguments

A a vector giving the x-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of average log intensities.
M a vector giving the y-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of log intensity ratios.
crit1 The number of points to be highlighted on the M vs A plot. If crit1 < 1, the crit1*100% spots with the smallest M values will be highlighted. If crit1 >= 1, the crit spots with the smallest M values are highlighted.
crit2 Similar to "crit1". If crit2 < 1, the crit2*100% spots with the largest M values will be highlighted. If crit2 >= 1, the crit2 spots with the smallest M values are highlighted.
nclass A single number giving the approximate number of intensity depedent groups to consider.
... graphical parameters may also be supplied as arguments to the function (see par).

Value

Points are added to the current plot.

Note

An M vs A plot must be constructed prior to the execution of this function.

See Also

plot.mva, stat.ma, lines, matlines, plot.confband.text, plot.confband.lines .

Examples

data(MouseArray)
## mouse.setup <- init.grid()
## mouse.data <- init.data()

plot.mva(mouse.data, mouse.setup) ## an M vs A plot 

mouse.lratio <- stat.ma(mouse.data, mouse.setup)

plot.confband.points(mouse.lratio$A, mouse.lratio$M)

## 2.5% of the spots with the smallest and largest M values are
## highlighted on the M vs A plot.