一、gglogo
install.packages("gglogo")library(gglogo)data(sequences)#加载sequences数据，是肽序列数据，是数据框格式
1.例一
ggplot(data = ggfortify(sequences, "peptide")) +##这一步很重要，ggfortif 将数据转换成绘制logo plots的格式，对sequences数据进行一个统计，下图展示数据情况geom_logo(aes(x = position, y = bits, group = element,#x是以position数据绘制横轴，y是以bits数据绘制纵轴，group是分组label = element, fill = interaction(Polarity, Water)),#label是标签，fill是填充颜色的分组alpha = 0.6) +#alpha是柱状图透明度scale_fill_brewer(palette = "Paired") +#颜色theme(legend.position = "bottom")#图例位置
2.例二
ggplot(data = ggfortify(sequences, "peptide", treatment = "class")) +geom_logo(aes(x=class, y=bits, group=element,label=element, fill=element)) +#根据element填充颜色facet_wrap(~position, ncol=18) +#根据position分面，成18列分布theme(legend.position = "bottom")
3.例三
ggplot(data = ggfortify(sequences, "peptide", treatment = "class")) +geom_logo(aes(x=position, y=bits, group=element, label=element, fill=element)) +facet_wrap(~class, ncol=1) +#根据class分面，成一theme_bw()#theme_bw 去掉背景色
4.例四
ggplot(data = ggfortify(sequences, "peptide", treatment = "class")) +geom_logo(aes(x=class, y=bits, group=element,label=element, fill=interaction(Polarity, Water))) +scale_fill_brewer("Amino-acids properties", palette="Paired") +facet_wrap(~position, ncol=18) +theme(legend.position="bottom") +xlab("") + ylab("Shannon information in bits")#xlab，ylab修改坐标轴名称
二、logo
用logo绘制简单的序列标志图
library(RColorBrewer)cols <- rep(brewer.pal(12, name="Paired"),22)logo(sequences$peptide) + aes(fill=element) +scale_fill_manual(values=cols)
