plotTIFF: Produce plots of the Illumina tiff images

Description

Produces a plot of an Illumina tiff image, which can be useful for observing spatial artifacts on an array and checking the alignment of spot centres features in the image.

Usage

plotTIFF(tiff, xrange = c(0, ncol(tiff)-1), yrange = c(0, nrow(tiff)-1), high = "cyan", low = "black", mid = NULL, ncolours = 100, log = TRUE, values = FALSE, textCol = "black", ...)

Arguments

tiff

Intended to the the result of readTIFF, but in reality can be any matrix

xrange

Range of X coordinates to plot.

yrange

Range of Y coordinates to plot.

high

Colour to plot the brightest pixels in the image.

low

Colour to plot the dimmest pixels.

mid

If specified the colour gradient will go from low to mid to high. If not specified then the gradient simply goes from low to high.

ncolours

Specify how many steps there should be in the gradient between the high and low colours

log

If TRUE the pixel values are logged before the colour gradient is created.

values

When set to TRUE each pixel in the image has it's value displayed over it. This should only be used when displaying a very small number of pixels as the text very quickly covers the entire image.

textCol

If values is TRUE this argument specifies the colour of the text.

...

Other graphical parameters specified in par

Value

A plot is produced on the current graphical device.

Details

This can be very slow, especially when the Cairo graphics library is being used. When using the Cairo library, if one is plotting a large tiff with 10s of millions of pixels, the plotting time increases from around 20 seconds to 5 minutes on an Intel Xeon E5420.

If running on a Linux system it is recommended to use:

x11(type = "Xlib")

before running plotTIFF(), on order to force the quicker plotting mechanism.

Of course it is debatable whether it is useful to plot all of those pixels, given that there are far more than can be displayed on a normal screen, and future revisions of the code may address this.