geom_helix {ggmsa} | R Documentation

## geom_helix

### Description

The layer of helix plot

### Usage

    geom_helix(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.
`...` | additional parameter

### Value

ggplot2 layers

### Author(s)

Lang Zhou

### Examples

    RF03120 <- system.file("extdata/Rfam/RF03120_SS.txt", package="ggmsa")
    RF03120_fas <- system.file("extdata/Rfam/RF03120.fasta", package="ggmsa")
    SS <- readSSfile(RF03120, type = "Vienna")
    ggmsa(RF03120_fas, font = NULL,border = NA,
        color = "Chemistry_NT", seq_name = FALSE) +
    geom_helix(SS)

[Package ggmsa version 1.0.0 Index]