绘制“序列标志”使用ggplot2？

Question

是否可以（合理）使用 ggplot2 绘制序列徽标图？

有一个基于“网格”的包可以做到这一点，称为“seqLogo ”，但我想知道是否有它的 ggplot2 版本。

谢谢。

Answer 1

ggseqlogo 应该是您要找的。我希望这可以减轻一些挫败感，我相信你们中的许多人在 R 中绘制序列徽标时都会遇到这样的挫败感

Answer 2

我正在提交一个 ggplot2 尝试，它与上面的 Leipzig/Berry 解决方案有些相似。这种格式稍微更接近标准语标。

但我的解决方案，以及我认为任何 ggplot2 解决方案，仍然存在不足，因为 ggplot2 无法控制绘图符号的纵横比。这是（我认为）生成序列徽标所需的核心功能，而 ggplot2 中缺少该功能。

另请注意：我使用了Jeremy Leipzig的答案中的数据，但我没有对小样本量或％进行任何更正GC 值不同于 50%。

require(ggplot2)
require(reshape2)

 freqs<-matrix(data=c(0.25,0.65,0.87,0.92,0.16,0.16,0.04,0.98,0.98,1.00,0.02,0.10,0.10,0.80,0.98,0.91,0.07,0.07,0.11,0.05,0.04,0.00,0.26,0.17,0.00,0.01,0.00,0.00,0.29,0.17,0.01,0.03,0.00,0.00,0.32,0.32,0.53,0.26,0.07,0.02,0.53,0.18,0.96,0.01,0.00,0.00,0.65,0.01,0.89,0.17,0.01,0.09,0.59,0.12,0.11,0.04,0.02,0.06,0.05,0.49,0.00,0.00,0.02,0.00,0.04,0.72,0.00,0.00,0.01,0.00,0.02,0.49),byrow=TRUE,nrow=4,dimnames=list(c('A','C','G','T')))

freqdf <- as.data.frame(t(freqs))

freqdf$pos = as.numeric(as.character(rownames(freqdf)))

freqdf$height <- apply(freqdf[,c('A', 'C','G','T')], MARGIN=1,
                       FUN=function(x){2-sum(log(x^x,base=2))})

logodf <- data.frame(A=freqdf$A*freqdf$height, C=freqdf$C*freqdf$height,
                     G=freqdf$G*freqdf$height, T=freqdf$T*freqdf$height, 
                     pos=freqdf$pos)

lmf <- melt(logodf, id.var='pos')

quartz(height=3, width=8)

ggplot(data=lmf, aes(x=as.numeric(as.character(pos)), y=value))  +
    geom_bar(aes(fill=variable,order=value), position='stack', 
        stat='identity', alpha=0.5) +
    geom_text(aes(label=variable, size=value, order=value, vjust=value),
        position='stack') +
    theme_bw()

quartz.save('StackOverflow_5438474.png', type='png')

这会产生以下图表：

Answer 3

我已经实现了 Charles Berry 设计的替代方案，它解决了下面评论部分中令人厌烦的讨论的 seqLogos 的一些弱点。它使用ggplot2：

library("devtools")
install_github("leipzig/berrylogo")
library("berrylogo")
freqs<-matrix(data=c(0.25,0.65,0.87,0.92,0.16,0.16,0.04,0.98,0.98,1.00,0.02,0.10,0.10,0.80,0.98,0.91,0.07,0.07,0.11,0.05,0.04,0.00,0.26,0.17,0.00,0.01,0.00,0.00,0.29,0.17,0.01,0.03,0.00,0.00,0.32,0.32,0.53,0.26,0.07,0.02,0.53,0.18,0.96,0.01,0.00,0.00,0.65,0.01,0.89,0.17,0.01,0.09,0.59,0.12,0.11,0.04,0.02,0.06,0.05,0.49,0.00,0.00,0.02,0.00,0.04,0.72,0.00,0.00,0.01,0.00,0.02,0.49),byrow=TRUE,nrow=4,dimnames=list(c('A','C','G','T')))
p<-berrylogo(freqs,gc_content=.41)
print(p)

Answer 4

就我而言，在 ggplot2 中没有直接的方法可以做到这一点。

不过，请查看 RWebLogo。这是我为 WebLogo python 库编写的 R 包装器。您可以从 CRAN 下载它，它托管在 github

简单示例：

# Load package
library('RWebLogo')

# Sample alignment
aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
# Plot logo to file
weblogo(seqs=aln, file.out='logo.pdf')

# Plot logo to R graphics device (uses generated jpeg logo and raster package)
weblogo(seqs=aln, plot=TRUE, open=FALSE, format='jpeg', resolution=600)

有关更多选项，请参阅 ?weblogo 或 ?plotlogo< /代码>

Answer 5

这是一个替代选项。 motiflogo 是 ggplot2 实现的主题（序列）标志的新表示形式。可以考虑两个方面。

1. 作为规范主题徽标表示
2. 作为 SNP 特定主题徽标表示

Answer 6

现在有一个 gglogo 包（也在 CRAN 上，另一个令人惊叹的 ggplot2 Heike Hofmann 的扩展）。

该包生成如下图：

library(ggplot2)
library(gglogo)
ggplot(data = ggfortify(sequences, "peptide")) +      
  geom_logo(aes(x=position, y=bits, group=element, 
     label=element, fill=interaction(Polarity, Water)),
     alpha = 0.6)  +
  scale_fill_brewer(palette="Paired") +
  theme(legend.position = "bottom")

该示例来自 https://github.com/heike/gglogo/blob/master/visual_test/logos.R 包装上有一份手稿：https://github.com/heike/logopaper/blob/master/logos.Rmd