DC Depth图

#gc%含量为横坐标，depth为纵坐标，从基因组中取一个窗口（如每1000bp,计算gc%和depth的平均值），上侧和右侧的直方图是单独的gc%和depth直方图#
#有污染序列的GC depth图#

> m <- read.table("GC-depth.txt")
> head(m)
    V1    V2
1 48.0 54.30
2 39.0 75.90
3 42.2 83.64
4 40.8 82.28
5 50.8 97.73
6 42.6 84.11
> nf <- layout(matrix(c(0,2,0,0,1,3),2,3,byrow = T),c(0,5,3,1),c(1,3,0,5),TRUE);
> layout.show(3

> par("mar")#mar边界#
[1] 5.1 4.1 4.1 2.1
> par(mar = c(5,5,0.5,0.5))
> x <- m[,1]
> y <- m[,2]
> xhist <- hist(x,breaks = 100,plot = F)
> yhist <- hist(y,breaks = floor(max(y)-0),plot = F)
> xhist$counts  #每个条目的频数值#
 [1]   1   0   0   1   0   0   1   0   0   1   3   0   3   0   6
[16]   3   7   4   4  12  14  10  15  21  33  12  27  30  43  46
[31]  62  62 122  84 138 121 225 160 314 272 451 311 512 385 656
[46] 460 711 497 710 506 664 440 584 309 413 201 218 123 111  64
[61]  52  25  29  10  13   5   5   2   1
> plot(x,y,xlab = "GC Content(%)",ylab = "Depth",pch=16,col="red",xlim = c(0,100),ylim = c(0,max(y)))
> par(mar=c(0,5,1,1))
> barplot(xhist$counts,space = 0,xlim = c(0,100)

> par(mar=c(5,0,1,1))
> barplot(yhist$counts,space = 0,horiz = T,ylim = c(0,max(y))

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提取码：jd6v
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《R语言与生物信息绘图》课程笔记