simplot {seqcombo} | R Documentation |
Sequence similarity plot
simplot( file, query, window = 200, step = 20, group = FALSE, id, sep, sd = FALSE )
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 |
ggplot object
guangchuang yu
fas <- system.file("examples/GVariation/sample_alignment.fa", package="seqcombo") simplot(fas, 'CF_YL21')