imageplot: imageplot for beadLevelData object

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Generates an image plot for data from a beadLevelData object.

Usage

imageplot(BLData, array = 1, transFun = logGreenChannelTransform, squareSize = NULL, useLocs = TRUE, horizontal = TRUE, low = "lightgreen", high = "darkgreen", ncolors = 100, zlim = NULL, legend = TRUE, ...)

Arguments

BLData	beadLevelData
array	integer specifying what section to plot
transFun	Function that defines how values from the BLData object are to be transformed prior to plotting.
squareSize	Numeric specifying how many pixels in the original image make up each square in the imageplot. If NULL, the function will guess a suitable value from the data.
useLocs	If TRUE the function will read the locs file associated with the section in order to include the physical properties of the section in the plot
horizontal	If TRUE the image will be plotted so that the longest edge of the section is on the x axis.
low	colour to use for lowest intensity
high	colour to use for highest intensity
ncolors	The number of colour graduations between high and low
zlim	numerical vector of length 2 giving the extreme values of 'z' to associate with colours 'low' and 'high'.
legend	logical, if TRUE, zlim and range of data is added to plot.
...	other arguments to plot

Details

Produces a standard imageplot for the specified section. The default, transformation logGreenChannelTransform, takes the log2 of the green channel. For two channel data, the red channel or log ratio can be plotted by logRedChannelTransform or logRatioTransform functions can be used. The user can also specify their own functions.

The default plotting orientation is such that the longest edge of the section is along the x axis. If horizontal = FALSE, the longest edge will by on the y axis and should match how the corresponding TIFF image from the BeadScan directory is orientated.

If locs = TRUE and locs file were made available to readIllumina, the segments that the section is comprised of will be visible (For expression BeadChips, each section is made of nine physically separate segments). The squareSize parameter will also be set appropriately.

As a result of both having identical function names this function can conflict with the imageplot method in 'limma'. If both packages are loaded, the function from whichever package was loaded last takes precedence. If the 'beadarray' imageplot() function is masking that from 'limma', one can directly call the 'limma' method using the command "limma::imageplot()". Alternatively, one can detach the 'beadarray' package using "detach(package:beadarray)". Similar techniques can be used if 'limma' is masking the 'beadarray' method.

Value

A ggplot object which is printed to screen by default

Author(s)

Mike Smith and Mark Dunning

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)

##By default the first array is plotted, here we plot the 2nd which should give a more interesting example
imageplot(exampleBLData, array=2)

}


## Not run: 

ip <- imageplot(exampleBLData, array=2, low="lightgreen", high="darkgreen", horizontal=FALSE)

ggsave(ip, filename="myimageplot.png")

ip2 <- imageplot(exampleBLData, array=2, low="lightgreen", high="darkgreen", horizontal=TRUE)

ggsave(ip2, filename="myimageplot2.png")



## End(Not run)

markdunning/beadarray-devel documentation built on May 21, 2019, noon