R: Perspective image of microarray spots statistic
arrayPersp
R Documentation
Perspective image of microarray spots statistic
Description
The function arrayPersp creates perspective images of shades of gray or colors that correspond to the values of a statistic for each spot on the array. The statistic can be the intensity log-ratio, a spot quality measure (e.g. spot size or shape), or a test statistic. This function can be used to explore whether there are any spatial effects in the data, for example, print-tip or cover-slip effects.
If mediancenter=TRUE, values of Statistic are median-centered.
col
List of colors such as that generated by Palettes. In addition to these color palettes functions, a new function myPalette was defined to generate color palettes from user supplied low, middle, and high color values.
zlim
Numerical vector of length 2 giving the extreme values of
z to associate with colors low and high of
myPalette. By default zlim is the range of
z. Any values of z outside
the interval zlim will be truncated to the relevant limit.
bar
If bar=TRUE, a calibration color bar is shown to the right of the image.
...
Graphical parameters can be given as arguments to function
persp.
N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the
values in 1:arrayCol*SpotCol
Value
An image is created on the current graphics device.
Note
People interested in tools dealing with array CGH analysis can
visit our web-page http://bioinfo.curie.fr.