arrayPlot {GLAD} | R Documentation |
The function arrayPlot
creates spatial 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.
arrayPlot.default <- function(Statistic, Col, Row, ArrCol, ArrRow, SpotCol, SpotRow, mediancenter=FALSE, col=myPalette("green", "red", "yellow"), contour=FALSE, nlevels=5, zlim=NULL, bar=c("none", "horizontal", "vertical"), layout=TRUE, ...) arrayPlot.arrayCGH <- function(arrayCGH, variable, mediancenter=FALSE, col=myPalette("green", "red", "yellow"), contour=FALSE, nlevels=5, zlim=NULL, bar=c("none", "horizontal", "vertical"), layout=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. |
contour |
If contour=TRUE , contour are plotted,
otherwise they are not shown. |
nlevels |
Numbers of levels added by contour if contour=TRUE . |
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=='horizontal' (resp. 'vertical' ), an
horizontal (resp. vertical) calibration color bar is shown to the
right of the image. |
layout |
If layout==TRUE plot layout is automatically set
when a color bar is asked for |
... |
Graphical parameters can be given as arguments to function
image . |
N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the
values in 1:arrayCol*SpotCol
This function is very similar to the
maImage
written by Sandrine Dudoit with
added options zlim
, mediancenter
and layout
.
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.
image
, contour
, arrayPersp
, myPalette
.
data(arrayCGH) pdf(file="arrayCGH.pdf",height=21/cm(1),width=29.7/cm(1)) arrayPlot(array2$Log2Rat, array2$Col, array2$Row, 4,4,21,22, main="Spatial Image of array CGH") dev.off() # object of class arrayCGH array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22)) class(array) <- "arrayCGH" arrayPlot(array,"Log2Rat", main="Spatial Image of array CGH")