plot_PDCP: Pairwise nucleotide Distance Correspondence Plot

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

Pairwise nucleotide Distance Correspondence Plot

Description

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, matrices of distances between pairs of sequences calculated for st1-e1 and st2-e2 regions

Usage

plot_PDCP(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 plot for two regions, dataframe with distances in region 1 and region 2

Examples

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

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