plot_PDCP_control: Control for Pairwise nucleotide Distance Correspondence Plot

In v-julia/recDplot: Visualisation of recombination events in nucleotide sequences using pairwise distance plots

Control for Pairwise nucleotide Distance Correspondence Plot

Description

Plots control for PDC plot. Control plot visualizes the correspondence of p-distances in subalignments with odd and even positions of original alignment.

Usage

plot_PDCP_control(dna_object, st1, e1, st2, e2)

Arguments

dna_object	list of DNA sequences produced by read.dna function of ape package (as.character = TRUE mode)
st1	start position of genome region 1
e1	end position of genome region 1
st2	start position of genome region 2
e2	end position of genome region 2

Value

list with ggplot object with control plot for two regions, dataframe with distances in concatenated odd and even positions of alignment

Examples

## Not run: 
alignment = read.dna(path/to/file, format="fasta", as.character=TRUE)
alignment[alignment=='-'] <- NA
plot_PDCP_control(alignment, 1, 500, 600, 1000)
## End(Not run)

v-julia/recDplot documentation built on Feb. 20, 2024, 1:59 p.m.