plotSpikeCI: plot spike concentration vs measured intensity

Description

plot spike known concentration and measured intensity of one array.

Usage

plotSpikeCI(spike, parameter,array = 1, bc = FALSE, area = TRUE,  meanpoint = TRUE,xlab = "log(Concentration)", ylab = "log(Intensity)", main = colnames(spike$R)[array], onlycalib = TRUE, xlim = NULL, ylim = NULL, pch = 19, cex = 0.2, meanpch = 21, meancex = 1, lwd = 1.5,  cy5col = "red", cy3col = "green", ...)

Arguments

spike

a SpikeList object.

parameter

a ParameterList object.

array

integer giving the array to be plotted.

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.

meanpoint

a logical value. TRUE is to show meanpoint of measured intensities with the same concentration on the plot. FALSE means not show.

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 of the plot.

pch

a integer code for one 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 0.4.

meanpch

a integer code for one of plotting characters or symbols for the meanpoints. Default is 21.

meancex

a numerical value giving the amount by which the meanpoints should be scaled relative to the default value. Default is 1.

lwd

width of the model curves. Default is 1.5.

cy5col

color of all symbols for cy5. Default is red.

cy3col

color of all symbols for cy3. Default is green.

...

other graphical parameters can be used in function plot.

Value

A plot is created on the current graphics device.

Details

The function plots spike concentration and measured intensity of one array. array number is specified by the argument array. It accepts the concentration of given array from the agrument spike, which is a SpikeList object. The measured intensities are calculated from spike. Four different ways can be used to calculate the measured intensities. Arguments bc and area are logical and their combinations are used for specifying the 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.

In order to help data visualization, meanpoints and model curve can be added on the plot. And the arguments meanpoint and parameter are correspond to these. The meadians of every group of measured intensities which have the same concentration are shown on the polt if meanpoint is true. Model curves of both dye are shown if the arguement parameter is specified after parameter estimation.

Examples

Run this code

# load data: spike
data(spike)

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

# use the default values for other parameters.
plotSpikeCI(spike,array=array)

# after parameter estimation, the model curves can be shown on the plot.
data(parameter)
plotSpikeCI(spike,parameter,array=array)