绘制序列标识图-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

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

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")

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

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

library(RColorBrewer)
cols <- rep(brewer.pal(12, name="Paired"),22)
logo(sequences$peptide) + aes(fill=element) + 
scale_fill_manual(values=cols)