## 1.设置当前工作目录
setwd("./ggmsa")
## 2.安装和导入R包
# install.packages("ggmsa")
library(ggmsa)
library(ggplot2)
## 3.R包简要信息
help(package = "ggmsa")
# Package: ggmsa
# Title: Plot Multiple Sequence Alignment using 'ggplot2'
# Version: 0.0.4
# Authors@R: c( person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")),
# person("Lang", "Zhou", email = "nyzhoulang@gmail.com", role = "aut"),
# person("Huina", "Huang", email = "1185796994@qq.com", role = "ctb"))
# Description: Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.
# Depends: R (>= 3.5.0)
# Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, stringr
# Suggests: ape, cowplot, ggtree, knitr, methods, seqmagick
# License: Artistic-2.0
# Encoding: UTF-8
# LazyData: true
# RoxygenNote: 7.1.0
# VignetteBuilder: knitr
# NeedsCompilation: no
# Packaged: 2020-05-28 08:15:32 UTC; ygc
# Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
# Lang Zhou [aut],
# Huina Huang [ctb]
# Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
# Repository: CRAN
# Date/Publication: 2020-05-28 10:50:10 UTC
# Built: R 3.6.3; ; 2020-05-29 14:03:22 UTC; windows
ls(package:ggmsa)
# [1] "available_colors" "available_fonts" "available_msa"
# [4] "facet_msa" "geom_asterisk" "geom_GC"
# [7] "geom_msa" "geom_seed" "geom_seqlogo"
# [10] "ggmotif" "ggmsa" "tidy_msa"
## 4.测试
# Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.
# Supports visualizing multiple sequence alignment of DNA and protein sequences using ggplot2 It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other ‘ggplot2’ plots, such as aligning a phylogenetic tree produced by ‘ggtree’ with multiple sequence alignment.
### 4.1 Load sample data
# Three sample data are shipped with the ggmsa package. Note that ggmsa supports not only fasta files but other objects as well. available_msa()can be used to list MSA objects currently available.
available_msa()
# files currently available:
# .fasta
# XStringSet objects from 'Biostrings' package:
# DNAStringSet RNAStringSet AAStringSet BStringSet DNAMultipleAlignment RNAMultipleAlignment AAMultipleAlignment
# bin objects from 'seqmagick' package:
# DNAbin AAbin
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")
path.package("ggmsa")
# [1] "C:/Users/lenovo/Documents/R/win-library/3.6/ggmsa"
# Visualizing Multiple Sequence Alignments #
### 4.2 The most simple code to use ggmsa:
?ggmsa
#@ 简单绘制
ggmsa(protein_sequences, start = 265, end = 300)
#@ 调整参数，实现个性化绘制多序列比对图
ggmsa(protein_sequences, start = 265, end = 300, font = "TimesNewRoman", color = "Clustal", char_width = 0.8, none_bg = T, seq_name = T)
ggmsa(protein_sequences, start = 265, end = 300, font = "TimesNewRoman", color = "Chemistry_AA", char_width = 0.8, none_bg = F)
# Colour Schemes #
available_colors()
# color schemes for nucleotide sequences currently available:
# Chemistry_NT Shapely_NT Taylor_NT Zappo_NT
# color schemes for AA sequences currently available:
# Clustal Chemistry_AA Shapely_AA Zappo_AA Taylor_AA
### 4.3 Clustal X Colour Scheme(Default)
#@ This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type.
ggmsa(protein_sequences, start = 320, end = 360, color = "Clustal")
### 4.4 Color by Chemistry
#@ Amino acids are colored according to their side chain chemistry:
ggmsa(protein_sequences, start = 320, end = 360, color = "Chemistry_AA")
### 4.5 Color by Shapely
#@ This color scheme matches the RasMol amino acid and RasMol nucleotide color schemes, which are, in turn, based on Robert Fletterick’s “Shapely models”.
ggmsa(protein_sequences, start = 320, end = 360, color = "Shapely_AA")
### 4.6 Color by Taylor
#@ This color scheme is taken from Taylor(Taylor 1997) and is also used in JalView(Waterhouse et al. 2009).
ggmsa(protein_sequences, start = 320, end = 360, color = "Taylor_AA")
### 4.7 Color by Zappo
#@ This scheme colors residues according to their physico-chemical properties, and is also used in JalView(Waterhouse et al. 2009).
ggmsa(protein_sequences, start = 320, end = 360, color = "Zappo_AA")
### 4.8 Font
#@ Several classic font for MSA are shipped in the package. In the same ways, you can use available_fonts() to list font currently available
available_fonts()
# font families currently available:
# helvetical mono TimesNewRoman DroidSansMono
# helvetical
ggmsa(protein_sequences, start = 320, end = 360, font = "helvetical", color = "Chemistry_AA")
# TimesNewRoman
ggmsa(protein_sequences, start = 320, end = 360, font = "TimesNewRoman", color = "Chemistry_AA")
# DroidSansMono
ggmsa(protein_sequences, start = 320, end = 360, font = "DroidSansMono", color = "Chemistry_AA")
#@ If you specify font = NULL, only tiles will be plot.
ggmsa(protein_sequences, start = 320, end = 360, font = NULL, color = "Chemistry_AA", seq_name = F)
ggmsa(protein_sequences, start = 320, end = 360, font = NULL, color = "Chemistry_AA", seq_name = T)
### 4.9 Characters width
#@ Characters width can be specified by char_width. Defaults is 0.9.
ggmsa(protein_sequences, start = 320, end = 360, char_width = 0.5, color = "Chemistry_AA")
### 4.10 Background
#@ Background can be specified by none_bg. If none_bg = TRUE, only the character will be plot.
ggmsa(protein_sequences, start = 320, end = 360, none_bg = TRUE) + theme_void()
### 4.11 Position Highligthed
#@ Position Highligthed can be specified by posHighligthed. The none_bg = FALSE when you specified position Highligthed by posHighligthed
# 不连续高亮
ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA",
posHighligthed = c(185, 190))
ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA", posHighligthed = c(180, 190, 200))
# 连续高亮
ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA",
posHighligthed = c(180:200))
### 4.12 Sequence names
#@ Sequence names Defaults is ‘NULL’ which indicates that the sequence name is displayed when font = NULL, but ‘font = char’ will not be displayed. If seq_name = TRUE the sequence name will be displayed when you need it.
ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA", seq_name = TRUE)
#2 If seq_name = FALSE the sequence name will not be displayed in any case.
ggmsa(protein_sequences, 164, 213, font = NULL, color = "Chemistry_AA", seq_name = FALSE)
## 5.结束
# RUNRPTEST("./ggmsa", rpackage = "ggmsa",install_method = "website", rpackage_repository = "cran")
sessionInfo()
# R version 3.6.3 (2020-02-29)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 18363)
#
# Matrix products: default
#
# locale:
# [1] LC_COLLATE=Chinese (Simplified)_China.936
# [2] LC_CTYPE=Chinese (Simplified)_China.936
# [3] LC_MONETARY=Chinese (Simplified)_China.936
# [4] LC_NUMERIC=C
# [5] LC_TIME=Chinese (Simplified)_China.936
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods
# [7] base
#
# other attached packages:
# [1] ggplot2_3.3.0 ggmsa_0.0.4
#
# loaded via a namespace (and not attached):
# [1] Rcpp_1.0.4.6 pillar_1.4.4 compiler_3.6.3
# [4] XVector_0.26.0 tools_3.6.3 zlibbioc_1.32.0
# [7] digest_0.6.25 packrat_0.5.0 lifecycle_0.2.0
# [10] tibble_3.0.1 gtable_0.3.0 pkgconfig_2.0.3
# [13] rlang_0.4.6 rstudioapi_0.11 seqmagick_0.1.3
# [16] parallel_3.6.3 withr_2.2.0 dplyr_0.8.5
# [19] stringr_1.4.0 Biostrings_2.54.0 S4Vectors_0.24.3
# [22] vctrs_0.3.0 IRanges_2.20.2 stats4_3.6.3
# [25] grid_3.6.3 tidyselect_1.1.0 glue_1.4.1
# [28] R6_2.4.1 purrr_0.3.4 tidyr_1.1.0
# [31] farver_2.0.3 magrittr_1.5 scales_1.1.1
# [34] ellipsis_0.3.1 BiocGenerics_0.32.0 assertthat_0.2.1
# [37] colorspace_1.4-1 labeling_0.3 stringi_1.4.6
# [40] munsell_0.5.0 crayon_1.3.4
#@ 两篇参考文献，有兴趣的同学读一下
# Taylor, W R. 1997. “Residual Colours: A Proposal for Aminochromography.” Protein Eng 10 (7): 743–46.
# Waterhouse, A. M., J. B. Procter, D. M. Martin, M Clamp, and G. J. Barton. 2009. “Jalview Version 2–a Multiple Sequence Alignment Editor and Analysis Workbench.” Bioinformatics 25 (9): 1189.
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