plotSpikeHI: plot hybridized target vs intensity

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

With final parameter setting, plot the amount of hybridized targets and intensities of calibration controls.

Usage

plotSpikeHI(spike, parameter, array = 1, xlab = "log(Hybridized)",
            ylab = "log(Intensity)", main = colnames(spike$R)[array],
            xlim = NULL, ylim = NULL, pch = 19, cex = 0.2, 
            cy5col = "black", cy3col = "black", noerror = TRUE,
            noepch = 19, noecex = 0.1, noecy5col = "lightpink",
            noecy3col = "lightblue", curve = TRUE, lwd = 1.5, 
            curvecy5col = "red", curvecy3col = "green", ...)

Arguments

spike	a SpikeList object.
parameter	a ParameterList object.
array	integer giving the array to be plotted.
xlab	a title for the x axis.
ylab	a title for the y axis.
main	an overall title for the plot.
xlim	the x limits (min,max) of the plot.
ylim	the y limits of the plot.
pch	an integer code for one of plotting characters or symbols for the spike data set. Default is 19.
cex	a numerical value giving the amount by which the points which indicate spike data set should be scaled relative to the default. Default is 0.2.
cy5col	color of points for cy5. Default is black.
cy3col	color of points for cy3. Default is black.
noerror	a logical value. If it is TRUE, plot the amount of hybridized targets assuming equal spot capacities. Default is TRUE.
noepch	pch for the points with equal spot capacities. Default is 19.
noecex	cex for the points with equal spot capacities. Default is 0.1.
noecy5col	color for the points with equal spot capacities of cy5. Default is lightpink.
noecy3col	color for the points with equal spot capacities of cy3. Default is lightblue.
curve	a logical value. If it is TRUE, plot final parameter setting. Default is TRUE.
lwd	width of the parameter curves. Default is 1.5.
curvecy5col	color of the parameter curves for cy5. Default is red.
curvecy3col	color of the parameter curves for cy3. Default is green.
...	other graphical parameters can be used in function 'plot'.

Details

The function plots hybridized targets vs measured intensities of one array. The argument array gives the array index to be plotted. The function accepts the spike concentrations from the argument spike and the estimated spot error for each spot from the argument parameter. The hyrbidized targets for each spot can be calculated by the following formula: formula.

The argument noerror says whether or not the hybridized targets, which are calculated by the above mentioned formula assuming equal spot capacities, are plotted. If they are plotted, other arguments like noepch,noecex,noecy5col and noecy3col are used to specify the type, the size and the color of the points.

Estimated parameter curves can be shown on the plot. Since model parameters are different for two colors, two parameter curves are expected for one array. The funciton accepts parameters of both colors from the argument parameter. If the curves are plotted, the arguments lwd, curvecy3col and curvecy5col are used to specify the width and color of the curves.

Details for the graphical parameters can be seen in function plot, points and curve.

Value

A plot is created on the current graphics device.

Author(s)

Hui Zhao

References

Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22: 1251-1258.

Examples

# load data: spike and parameter
data(spike)
data(parameter)

# specify the array to be plotted.
array <- 1

# use the default values for other parameters
plotSpikeHI(spike,parameter,array=array)

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.