ENc.GC3plot {vhcub}

ENc-GC3 scatterplot.

Description

Make an ENc-GC3 scatterplot. Where the y-axis represents the ENc values and the x-axis represents the GC3 content. The red fitting line shows the expected ENc values when codon usage bias affected solely by GC3.

Usage

ENc.GC3plot(enc.df, gc.df)

Arguments

enc.df

a data frame with ENc values.

gc.df

a data frame with GC3 values.

Details

For more information about ENc-GC3 plot Butt et al., 2016.

Value

A ggplot object.

Author(s)

Ali Mostafa Anwar [e-mail] and Mohmed Soudy [e-mail]

Examples

# read DNA from fasta file
fasta <- fasta.read("virus.fasta", "host.fasta")
fasta.v <- fasta[[1]]
enc.df.virus <- ENc.values(fasta.v)


gc.df <- GC.content(fasta.v)

ENc.GC3plot(enc.df.virus, gc.df)