nandb (version 0.2.1)

KmerPlot: A brightness image with a different colour for each kmer.

Description

Make a colour image based on a brightness image where each kmer has its own colour. This requires you te specify the brightness of a monomer (which should be greater than 1).

Usage

KmerPlot(brightness.mat, monomer.brightness, log.trans = FALSE)

Arguments

brightness.mat

The brightness matrix.

monomer.brightness

The (median) brightness of a monomer.

log.trans

Do you want to log-transform the colour scaling?

This is a ggplot2 object and can be manipulated thus.

Examples

# NOT RUN {
library(EBImage)
img <- ReadImageData(system.file('extdata', '50.tif', package = 'nandb'))
display(normalize(img[, , 1]), method = 'raster')
brightness <- Brightness(img, tau = NA, mst = "Huang")
KmerPlot(brightness, 1.02)
KmerPlot(brightness, 1.12)
KmerPlot(brightness, 100)
KmerPlot(brightness, 1.02, log.trans = TRUE)
KmerPlot(MedianFilterB(brightness), 1.02)

# }