simplot {ggmsa} | R Documentation

## 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

### Author(s)

guangchuang yu

### Examples

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

[Package ggmsa version 1.0.0 Index]