arrayPersp {GLAD} | R Documentation |
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.
arrayPersp.default(Statistic, Col, Row, ArrCol, ArrRow, SpotCol, SpotRow, mediancenter=FALSE, col=myPalette("green","red","yellow"), arrayPersp.arrayCGH(arrayCGH, variable, mediancenter=FALSE, col=myPalette("green","red","yellow"), zlim=zlim, bar=TRUE, ...)
arrayCGH |
Object of class arrayCGH . |
variable |
Variable to be plotted |
Statistic |
Statistic to be plotted. |
Col |
Vector of columns coordinates. |
Row |
Vector of rows coordinates. |
ArrCol |
Number of columns for the blocs. |
ArrRow |
Number of rows for the blocs. |
SpotCol |
Number of column for each bloc. |
SpotRow |
Number of rows for each bloc. |
mediancenter |
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
An image is created on the current graphics device.
People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.
Philippe Hupé, glad@curie.fr.
data(arrayCGH) # object of class arrayCGH array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22)) class(array) <- "arrayCGH" arrayPersp(array,"Log2Rat", main="Perspective image of array CGH", box=FALSE, theta=110, phi=40)