Plots for John Aach

DNA abundance

ggplot(ngs, aes(x = Count.DNA)) + geom_histogram(binwidth = 100) + theme_bw()

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Not negative binomial, more like lognormal.

DNA abundance vs. GC

ggplot(ngs, aes(x = Count.DNA, y = GC)) + geom_point(alpha = 0.1) + theme_bw()

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Perhaps a weak corrleation between increased reads and increased GC, but as I show below, it has more to do with low GC leading to high expression leading to slower growth rates.

DNA abundance vs. Protein level

ggplot(ngs, aes(x = Count.DNA, y = Prot)) + geom_point(alpha = 0.1) + theme_bw()

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DNA count versus Protein level. Highly expressed constructs have fewer DNA reads (i.e. they grow more slowly).

DNA abundance vs. RNA level

ggplot(ngs, aes(x = Count.DNA, y = log10(RNA), color = Promoter)) + geom_point(alpha = 0.1) + 
    theme_bw()

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DNA count versus RNA level (RNA/DNA). The stronger promoter (red) has more constructs with fewer reads.