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.

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