image {marray} | R Documentation |
We encourage users calling "image" rather than "maImage". The name of
the arguments are change slightly.
The function image
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.
## S4 method for signature 'marrayRaw': image(x, xvar = "maM", subset = TRUE, col, contours=FALSE, bar = TRUE, overlay=NULL, ol.col=1, ...) ## S4 method for signature 'marrayNorm': image(x, xvar = "maM", subset = TRUE, col, contours=FALSE, bar = TRUE, overlay=NULL, ol.col=1, ...)
x |
Microarray object of class "marrayRaw" ,
"marrayNorm" |
xvar |
Name of accessor function for the spot statistic of interest,
typically a slot name for the microarray object x , such as
maM . |
subset |
A "logical" or "numeric" vector indicating the subset of spots to display on the image. |
col |
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. |
bar |
If bar=TRUE , a calibration color bar is shown to the right of the image. |
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 . |
This function calls the general function maImage.func
,
which is not specific to microarray data. If there are more than one
array in the batch, the plot is done for the first array, by
default. Default color palettes were set for different types of spot
statistics using the maPalette
function. When
x=c("maM", "maMloc", "maMscale")
, a green-to-red color palette
is used. When x=c("maGb", "maGf", "maLG")
, a white-to-green
color palette is used. When x=c("maRb", "maRf", "maLR")
, a
white-to-red color palette is used. The user has the option to
overwrite these parameters at any point.
A list with elements
x.col |
vector of colors to be used for calibration color bar. |
x.bar |
vector of values to be used for calibration color bar. |
summary |
six number summary of the spot statistics, from the function summary . |
Jean Yang and Sandrine Dudoit
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.
maImage
, maImage.func
,
maColorBar
, maPalette
# Examples use swirl dataset, for description type ? swirl data(swirl) # Microarray color palettes Gcol <- maPalette(low = "white", high = "green", k = 50) Rcol <- maPalette(low = "white", high = "red", k = 50) BYcol <- maPalette(low = "blue", mid="gray", high = "yellow", k = 50) # Color images of green and red background and foreground intensities ##image(swirl[, 2], xvar ="maGb") ##image(swirl[, 2], xvar ="maGf", subset = TRUE, col = Gcol, contours = FALSE, bar = TRUE, main="Swirl array 93") ##image(swirl[, 1], xvar ="maRb", contour=TRUE) ##image(swirl[, 4], xvar ="maRf", bar=FALSE) # Color images of pre-normalization intensity log-ratios ##image(swirl[, 1]) # Color images with overlay spots ##image(swirl[, 3], xvar = "maA", overlay = maTop(maA(swirl[, 3]), h = 0.1, l = 0.1), bar = TRUE, main = "Image of A values with % 10 tails highlighted") # Color image of print-tip-group ##image(swirl[, 1],xvar = "maPrintTip")