plotSpikeCI {CALIB} | R Documentation |
plot spike known concentration and measured intensity of one array.
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", ...)
spike |
a SpikeList object. |
parameter |
a ParameterList object. |
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 . |
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 . |
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.
A plot is created on the current graphics device.
Hui Zhao
see graphic functions plot
, par
# 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)