maImage.func {marray} | R Documentation |
This function 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 M, 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. This function is called by maImage
.
maImage.func(x, L, subset=TRUE, col=heat.colors(12), contours=FALSE, overlay=NULL, ol.col=1, ...)
x |
A "numeric" vector of spot statistics. |
L |
An object of class "marrayLayout" , if L is
missing we will assume the dimension of x. |
subset |
A "logical" or "numeric" vector indicating the subset of spots to display on the image. |
col |
A list of colors such as that generated by rainbow , heat.colors , topo.colors , terrain.colors , or similar functions. In addition to these color palette functions, a new function maPalette was defined to generate color palettes from user supplied low, middle, and high color values. |
contours |
If contours=TRUE , contours are plotted,
otherwise they are not shown. |
overlay |
A logical vector of spots to be highlighted on the image plots. |
ol.col |
Color of the overlay spots. |
... |
Optional graphical parameters, see par . |
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.
image
, maImage
, maColorBar
, maPalette
.
# See examples for image.