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", ...)SpikeList object.ParameterList object.TRUE, plot the amount of hybridized targets
assuming equal spot capacities. Default is TRUE. TRUE, plot final parameter setting.
Default is TRUE.plot'. 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.
# 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)
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