simplot

Sequence similarity plot

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

guangchuang yu

Examples

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