simplot: simplot

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

simplot

Description

Sequence similarity plot

Usage

simplot(
  file,
  query,
  window = 200,
  step = 20,
  group = FALSE,
  id,
  sep,
  sd = FALSE,
  smooth = FALSE,
  smooth_params = list(method = "loess", se = 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.(eg. For "A-seq1,A-seq-2,B-seq1 and B-seq2", using sep = "-" and id = 1 to divide sequences into groups A and B)
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
smooth	FALSE(default)or TRUE; whether display smoothed spline.
smooth_params	a list that add params for geom_smooth, (default: smooth_params = list(method = "loess", se = FALSE))

Value

ggplot object

Author(s)

guangchuang yu

Examples

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

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.