geom_helix: geom_helix

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

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)

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