其他
R可视化——ggseqlogo包绘制序列分析图
安装、加载R包
rm(list=ls())#安装包install.packages("ggseqlogo")#加载包library(ggseqlogo)数据
支持序列与矩阵两种格式的文件，以以ggseqlogo包自带示例数据ggseqlogo_sample为例：
data(ggseqlogo_sample)#DNA数据df1<-pfms_dna#氨基酸数据df2<-seqs_aa#序列格式df3<-seqs_dna$MA0011.1#矩阵格式——代表碱基位置及相应碱基在该位置的出现次数df4<-pfms_dna$MA0031.1ggseqlogo包绘图参数
1、基本参数查看
??ggseqlogo#查看参数ggseqlogo(data, facet = "wrap", scales = "free_x", ncol = NULL, nrow = NULL, ...)2、基本序列分析图绘制
ggseqlogo(df1)ggseqlogo(df3)3、方法的选择——“bits”(默认)和“probability”
p1<-ggseqlogo(df3,method="bits")p2<-ggseqlogo(df3,method="probability")cowplot::plot_grid(p1,p2,ncol=1)4、绘制多个图时通过facet与ncol控制
ggseqlogo(df1, facet = "wrap",ncol = 1)ggseqlogo(df1, facet = "wrap",ncol = 2)5、序列类型的指定
#通过seq_type参数指定序列类型，默认为“auto”自动识别，可选择"aa"、"dna"、"rna"ggseqlogo(df1, facet = "wrap",ncol = 2, seq_type="dna")ggseqlogo(df2, facet = "wrap",ncol = 2, seq_type="aa")6、配色方案
#通过col_scheme参数设置，具体配色方案通过?list_col_schemes查看list_col_schemes(v = T)ggseqlogo(df1,col_scheme='clustalx')ggseqlogo(df1,col_scheme='taylor')7、自定义配色方案——通过make_col_scheme参数实现，有离散型与连续性两种方式
#离散型配色col1<-make_col_scheme(chars = c("A","G", "T", "C"), groups = c("g1","g2", "g3","g4"), cols = c("red","green","blue","yellow"))ggseqlogo(df1,col_scheme=col1)#连续型配色col2<-make_col_scheme(chars=c("A","G", "T", "C"), values=1:4, name='group')ggseqlogo(df1,col_scheme=col2)8、字体设置
#通过font参数实现，可通过?list_fonts查看内置字体list_fonts(v = T)a<-ggseqlogo(df3,font="xkcd_regular")b<-ggseqlogo(df3,font="roboto_slab_regular")c<-ggseqlogo(df3,font="helvetica_regular")d<-ggseqlogo(df3,font="helvetica_light")cowplot::plot_grid(a,b,c,d,ncol=2)9、字母宽度设置
#通过stack_width参数设置a<-ggseqlogo(df3,stack_width=1)b<-ggseqlogo(df3,stack_width=0.5)cowplot::plot_grid(a,b,ncol=1)10、注释——与ggplot2注释原理一致
p1<-ggplot2::ggplot()+geom_logo(df3)+theme_logo()#可视化p1#添加文字注释p1+ggplot2::annotate("text", x=6, y=1, label="This is a text\n annotation!")#添加线条p1+ggplot2::annotate("segment", x=1, xend = 3, y=1.5, yend = 1.5, size=3)#添加图形注释p1+ggplot2::annotate("rect", xmin = 6.5, xmax = 7.5, ymin = -0.05, ymax = 0.8, alpha=0.2, col="grey", fill="green")绘图模板代码
#模板代码library(ggplot2)col1<-make_col_scheme(chars = c("A","G", "T", "C"), groups = c("g1","g2", "g3","g4"), cols = c("red","green","blue","yellow"))#自定义配色ggplot()+geom_logo(df1$MA0018.2,#数据 method="bits",#方法 seq_type="dna",#序列类型 col_scheme=col1,#配色方案 font="xkcd_regular",#字体 stack_width=0.8#字母宽度 )+ annotate("text", x=5.5, y=2, color='red',label="This is a text\n annotation!")+ annotate("segment", x=4.5, xend = 6.5, y=1.6, yend = 1.6, size=3)+ annotate("rect", xmin = 2.5, xmax = 3.5, ymin = -0.05, ymax = 2.05, alpha=0.2, col="grey", fill="green")+ theme_logo()爱我请给我好看!