imageplot {beadarray} | R Documentation |
Plots an image plot of a bead level data object.
imageplot(BLData, array = 1, nrow = 100, ncol = 100, low= NULL, high = NULL, ncolors = 123, whatToPlot ="G", log=TRUE, zlim=NULL, main=whatToPlot, method="illumina", n = 3, trim=0.05, legend=TRUE, ...)
BLData |
Object of class BLData |
array |
array to plot |
nrow |
How many rows should the array be divided into |
ncol |
How many columns should the array be divided into |
low |
Color for area of lowest intensity |
high |
color for area of highest intensity |
ncolors |
The number of color graduations between high and low |
whatToPlot |
character string specifying which intensities/values
to plot. See getArrayData for a list of the possibilities |
log |
if TRUE, log2 intensities are plotted |
zlim |
numerical vector of length 2 giving the extreme values of 'z' to associate with colors 'low' and 'high'. |
main |
character string for plot title |
method |
chracter string specifying the summarisation method to
use. Only applicable when whatToPlot="residG" , "residR"
or "residM" . Refer to help createBeadSummaryData help
page for further information. |
n |
use n median absolute deviations from the median as a
cut-off for outliers. Only applicable when
whatToPlot="residG" , "residR" or "residM" .
Refer to help createBeadSummaryData help page for further
information. |
trim |
fraction of intensities to remove from the bead summary
calculations. Only applicable when whatToPlot="residG" ,
"residR" or "residM" . Refer to
createBeadSummaryData help page for further information. |
legend |
logical, if TRUE , zlim and range of data
is added to plot. |
... |
other graphical parameters to plot that can be specified |
Because of the high volume of bead level data, this function works by mapping a grid (who's size is specified by the nrow and ncol) arguments and averages the intensities of the beads within each section of this grid.
The number of rows and columns may change the appearance of the
plots. If the array is divided into too many squares it will be difficult
to detect changes. We recommend using nrow=20
and
ncol=200
for whole genome arrays, and nrow=100
ncol=100
for arrays on a SAM.
An imageplot of the log base 2 foreround intensities is produced by default.
Other values can be plotted by changing the whatToPlot
argument.
Plot is produced on current graphical device.
Mike Smith, Mark Dunning
data(BLData) imageplot(BLData)