plotSpikeRG: plot spike intensity R vs G

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

Description

plot red intensity vs green intensity of spikes.

Usage

plotSpikeRG(spike,parameter,RG,array = 1, bc = FALSE, area = TRUE,
            xlab = "log(Rintensity)", ylab = "log(Gintensity)",
            main = colnames(spike$R)[array], onlycalib = FALSE, 
            xlim = NULL, ylim = NULL, pch = 19, cex = 0.3, col = "black", 
            allpch = 19, allcex = 0.05, allcol = "lightgrey", diag = TRUE,
            diagcol = "grey", diaglwd = 1, curvecol = "blue",
            curvelwd = 1.5, calibtype = 1, adjusttype = 4, ...)

Arguments

spike	a SpikeList object.
parameter	a ParameterList object.. If parameter argument is sepcified, model curves are shown on the plot.
RG	a RGList_CALIB object. If parameter argument is specified, this argument is obligated. More description in Detail section.
array	integer giving the array to be plotted.
bc	a logical value. TRUE means background corrected measured intensities are used. Default is FALSE.
area	a logical value. TRUE means spot area is used to calculate measured intensities. Namly, measured intensities are calculated by foreground intensities(or background corrected intensities, if bc is TRUE) multiply spot area. FALSE means spot area is not used. Default is TRUE.
xlab	a title for the x axis.
ylab	a title for the y axis.
main	an overall title for the plot.
onlycalib	a logical value. TRUE means only the calibration controls are on the plot. FALSE means to plot all the spikes
xlim	the x limits (min,max) of the plot.
ylim	the y limits (min,max) of the plot.
pch	an integer code for one of a set of plotting characters or symbols for the spike data set. Default is 21.
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 0.3.
col	the color of the points indicating spike data set. Default is black.
allpch	an integer code for one of a set of plotting characters or symbols for the spike data set. Default is 19.
allcex	a numerical value giving the amount by which the points which indicate all data set should be scaled relative to the default. Default is 0.05.
allcol	the color of the points indicating all data set. Default is lightgrey.
diag	a logical value. Add diagonal on the plot if it is TRUE. Default is TRUE.
diagcol	the color of the diagonal. Default is grey.
diaglwd	the width of the diagonal. Default is 1.
curvecol	the color of the model curves. Default is blue.
curvelwd	the width of the model curves for calibration control spikes. Default is 1.5.
calibtype	the line type of the model curves for calibration control spikes. Default is 1.
adjusttype	the line type of the model curves (using parameter after adjustment) for calibration control spikes. Default is 4.
...	other graphical parameters can be used in function plot.

Details

The function plots red vs green measured intensities of spikes of one array. The argument array gives the array index to be plotted.

If parameter estimation is done, the model curves can be plotted by giving the argument parameter. And if the argument parameter is specified, the argument RG is obligated. The combination of these two arguments is used to compare how the model fits to the spike and to the whole data set. More details about the usage of this function refers to the readme file of this package.

It supports different ways to calculate the measured intensities. Arguments bc and area are logical and their combinations are used for specifying four differents ways. bc indicates using background correction or not. area indicates multipling spot area or not. The default value of these two arguments are bc = FALSE and area = TRUE.

see other graphic functions for the other arguments.

Value

A plot is created on the current graphics device.

Author(s)

Hui Zhao

Examples

# load data: spike
data(spike)

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

# use the default values for other arguments
plotSpikeRG(spike,array=array)

# after parameter estimation, the model curves can be shown on the plot.
data(parameter)
data(RG)
plotSpikeRG(spike,parameter,RG)

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