plot_PDCP_with_control: Pairwise nucleotide Distance Correspondence Plot with control

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

Pairwise nucleotide Distance Correspondence Plot with control

Description

This function plots PDC plot and its control on the same figure. Each dot corresponds to a pair of nucleotide distances between the same pair of genomes in two genomic regions - with alignment positions st1-e1 and st2-e2 (see axis). Returns list with ggplot and dataframe with pairwise distances calculated for st1-e1 and st2-e2 regions

Usage

plot_PDCP_with_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 PDC and control plot for two regions, dataframe with distances in two regions of alignment and 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_with_control(alignment, 1, 500, 600, 1000)
## End(Not run)

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