ggmsa (version 1.0.2)

simplot: simplot

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

Examples

# NOT RUN {
fas <- system.file("extdata/GVariation/sample_alignment.fa", package="ggmsa")
simplot(fas, 'CF_YL21')
# }