phsc.plot.phyloscan: Plot phyloscan

In olli0601/Phyloscanner.R.utilities:

Plot phyloscan

Description

This function generates scan plots that summarize reconstructed viral phylogenetic relationships of two individuals. Several pairs of individuals can be processed simultaneously. For each pair of individuals, the scan plot shows the phylogenetic distance on the y-axis and topological relationship in colours between subgraphs from both individuals in each deep-sequence phylogeny across the genome. The genomic position on the x-axis indicates the start of each 250bp read alignment.

Usage

phsc.plot.phyloscan(
  rpw2,
  id.cols = c("ID1", "ID2"),
  ylim = NULL,
  cols.typet = NULL
)

Arguments

rpw2	data.table containing the basic phyloscanner statistics for each genomic window.
id.cols	name of columns in rpw2 that identify the two individuals
ylim	limits of y-axis.
cols.typet	colour for each phylogenetic relationship type

Value

ggplot object

olli0601/Phyloscanner.R.utilities documentation built on April 21, 2024, 1:59 p.m.