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(x, M, crit1=0.025, crit2=crit1, nclass=10, col.ex, ...)

Arguments

x 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. ie A
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.
col.ex A color for extreme points
... 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. 

[Package sma version 0.5.15 Index]