R: Color image for cDNA microarray spot statistics
image
R Documentation
Color image for cDNA microarray spot statistics
Description
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.
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.
colorinfo
A logical value indicating whether the function
should return the color scale information.
...
Optional graphical parameters, see par.
Details
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.
Value
If colorinfo is set to TRUE, the following list with elements will be returned.
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.
Author(s)
Jean Yang and Sandrine Dudoit
References
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.
See Also
maImage, maImage.func,
maColorBar, maPalette
Examples
# 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")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(marray)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/marray/image.Rd_%03d_medium.png", width=480, height=480)
> ### Name: image
> ### Title: Color image for cDNA microarray spot statistics
> ### Aliases: image,marrayRaw-method image,marrayNorm-method
> ### Keywords: hplot
>
> ### ** Examples
>
> # 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")
>
>
>
>
>
>
> dev.off()
null device
1
>