simplot: simplot

In seqcombo: Visualization Tool for Sequence Recombination and Reassortment

Description

Sequence similarity plot

Usage

simplot(file, query, window = 200, step = 20, group = FALSE, id, sep,
  sd = FALSE)

Arguments

file	alignment fast file
query	query sequence
window	sliding window size (bp)
step	step size to slide the window (bp)
group	whether grouping sequence
id	position to extract id for grouping; only works if group = TRUE
sep	separator to split sequence name; only works if group = TRUE
sd	whether display standard deviation of similarity among each group; only works if group=TRUE

Value

ggplot object

Author(s)

guangchuang yu

Examples

fas <- system.file("examples/GVariation/sample_alignment.fa", package="seqcombo")
simplot(fas, 'CF_YL21')

Example output

sh: 1: cannot create /dev/null: Permission denied

seqcombo documentation built on Nov. 8, 2020, 6:27 p.m.