# Author: Benben Miao

# Email: [email protected]

# Rversion: 4.2.0

# Date: 2022-11-30

# -> 0. Install and Library

# install.packages(c("ggplot2", "ggsci"))

# BiocManager::install("ggmsa")

library(ggplot2)

library(ggsci)

library(ggmsa)

# <- 0. Install and Library

options(warn = 1)

# -> 1. File Read

# msa_dna = "data/MSA/MSA_DNA.fasta"

# msa_rna = "data/MSA/MSA_miRNA.fasta"

# msa_aa = "data/MSA/MSA_AA.fasta"

msa_file = "data/BundleMSA/Gram-positive_AKL.fasta"

# <- 1. File Read

# -> 2. Data Operation

# protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")

# miRNA_sequences <- system.file("extdata", "seedSample.fa", package = "ggmsa")

# nt_sequences <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa")

# <- 2. Data Operation

# -> 3. Plot Parameters

bundleColor <- "#0088EE"

# ColorPicker

# <- 3. Plot Parameters

# # -> 4. Plot

p <- ggSeqBundle(

msa_file,

line_widch = 0.3,

line_thickness = 0.3,

line_high = 0,

spline_shape = 0.3,

size = 0.5,

alpha = 0.2,

bundle_color = bundleColor,

lev_molecule = c("-", "A", "V", "L", "I", "P", "F", "W", "M", "G", "S", "T", "C",

"Y", "N", "Q", "D", "E", "K", "R", "H")

)

# # <- 4. Plot

# -> 5. Save parameters

pdf_name = "results.pdf"

jpeg_name = "results.jpeg"

device_pdf = "pdf"

device_jpeg = "jpeg"

# "pdf", "jpeg", "tiff", "png", "bmp", "svg"

width = 10.0

height = 6.18

units = "in"

# "in", "cm", "mm", "px"

dpi <- 300

# <- 5. Save parameters

# -> 6. Save Image

ggsave(

filename = pdf_name,

plot = p,

device = device_pdf,

path = NULL,

scale = 1,

width = width,

height = height,

units = units,

dpi = 300,

limitsize = TRUE

)

ggsave(

filename = jpeg_name,

plot = p,

device = device_jpeg,

path = NULL,

scale = 1,

width = width,

height = height,

units = units,

dpi = 300,

limitsize = TRUE

)

# <- 6. Save Image