plot.confband.text {sma}R Documentation

Add Selected Text to an M vs A Plot

Description

`text' draws the strings given in the vector `labs' at the coordinates given by `M' and `A'

Usage

plot.confband.text(x, M, crit1=0.025, crit2=crit1, nclass=10,
labs=NULL, output=FALSE, ...)  

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 largest M values are highlighted.
nclass A single number giving the approximate number of intensity depedent groups to consider.
labs one or more character strings or expressions specifying the text to be written. If this string is not specified, by default the index of the vector `M' will be used.
output logical, defaulting to `FALSE'. If `TRUE' a vector containning the index to the vector `M' that are highlighted.
... graphical parameters may also be supplied as arguments to the function (see par).

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.lines, plot.confband.points .

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.text(mouse.lratio$A, mouse.lratio$M)
## 2.5% of the spots with the largest and smallest M values are
## highlighted on the M vs A plot, and each spot is assigned the
## default label of its corresponding index value. 

[Package sma version 0.5.15 Index]