gghelix {ggmsa} | R Documentation

## gghelix

### Description

Plots nucleltide secondary structure as helices in arc diagram

### Usage

    gghelix(helix_data, color_by = "length", overlap = FALSE)

### Arguments

`helix_data` | a data frame. The file of nucleltide secondary structure and then read by readSSfile().
`color_by` | generate colors for helices by various rules, including integer counts and value ranges one of "length" and "value"
`overlap` | Logicals. If TRUE, two structures data called predict and known must be given(eg:heilx_data = list(known = data1, predicted = data2)), plots the predicted helices that are known on top, predicted helices that are not known on the bottom, and finally plots unpredicted helices on top in black.

### Value

ggplot object

### Author(s)

Lang Zhou

### Examples

    RF03120 <- system.file("extdata/Rfam/RF03120_SS.txt", package="ggmsa")
    helix_data <- readSSfile(RF03120, type = "Vienna")
    gghelix(helix_data)

[Package ggmsa version 1.0.0 Index]