snp曼哈顿图绘制

使用CMplot包绘制环形曼哈度图

安装并加载所需R包

install.packages("CMplot")
library(CMplot)

基本用法

CMplot(Pmap, col=c("#377EB8", "#4DAF4A", "#984EA3", "#FF7F00"),
      bin.size=1e6, bin.max=NULL, pch=19, band=1, cir.band=0.5, H=1.5,
      ylim=NULL, cex.axis=1, plot.type="b", multracks=FALSE, cex=c(0.5,1,1),
      r=0.3, xlab="Chromosome", ylab=expression(-log[10](italic(p))), xaxs="i",
      yaxs="r", outward=FALSE, threshold = NULL, threshold.col="red",
      threshold.lwd=1, threshold.lty=2, amplify= TRUE, chr.labels=NULL,
      signal.cex = 1.5, signal.pch = 19, signal.col="red", signal.line=1,
      cir.chr=TRUE, cir.chr.h=1.5, chr.den.col=c("darkgreen", "yellow", "red")
      , cir.legend=TRUE, cir.legend.cex=0.6, cir.legend.col="black",
      LOG10=TRUE, box=FALSE, conf.int.col="grey", file.output=TRUE,
      file="jpg", dpi=300, memo="")

常用参数

Pmap    输入数据文件
col 设置不同染色体中点的颜色
cex 设置点的大小
pch 设置点的形状
band    设置不同染色体之间的间隔
H   设置每个圈的高度
ylim    设置y轴的范围
bin.size    设置SNP密度图中的窗口大小
cex.axis    设置坐标轴字体和标签字体的大小
plot.type   设置不同的绘图类型，可以设定为 "d", "c", "m", "q" or "b"
multracks   设置是否需要绘制多个track
r   设置圈的半径大小
xlab    设置x轴标签
ylab    设置y轴标签
outward 设置点的朝向是否向外
threshold   设置阈值并添加阈值线
threshold.col   设置阈值线的颜色
threshold.lwd   设置阈值线的宽度
threshold.lty   设置阈值线的类型
amplify 设置是否放大显著的点
signal.cex  设置显著点的大小
signal.pch  设置显著点的形状
signal.col  设置显著点的颜色
chr.labels  设置染色体的标签
chr.den.col 设置SNP密度图的颜色
cir.band    设置环状曼哈度图中不同染色体之间的间隔
cir.chr 设置是否显示染色体的边界
cir.chr.h   设置染色体边界的高度
cir.legend  设置是否显示图例
cir.legend.cex  设置图例字体的大小
cir.legend.col  设置图例的颜色
LOG10   设置是否对p-value取log10对数
conf.int.col    设置QQ图中置信区间的颜色
file.output 设置是否输出图片
file    设置输出图片的格式，可以设定为"jpg", "pdf", "tiff"
dpi 设置输出图片的分辨度
memo    设置输出图片文件的名字

加载并查看示数据

data(pig60K)
head(pig60K)
          SNP Chromosome Position    trait1     trait2     trait3
1 ALGA0000009          1    52297 0.7738187 0.51194318 0.51194318
2 ALGA0000014          1    79763 0.7738187 0.51194318 0.51194318
3 ALGA0000021          1   209568 0.7583016 0.98405289 0.98405289
4 ALGA0000022          1   292758 0.7200305 0.48887140 0.48887140
5 ALGA0000046          1   747831 0.9736840 0.22096836 0.22096836
6 ALGA0000047          1   761957 0.9174565 0.05753712 0.05753712

基本数据格式：

前三列分别为SNP的名称，所在染色体，SNP的位置，
后面每列为不同性状的P值，每个性状单独一列

默认绘图(分别绘制出SNP密度图，曼哈顿图，环形曼哈顿图和QQ图)

CMplot(pig60K)

单独绘制SNP密度图

CMplot(pig60K,plot.type = "d",bin.size = 1e6, col = c("darkgreen","yellow","red"))

绘制单性状曼哈顿图

CMplot(pig60K,plot.type = "m",threshold = c(0.01,0.05)/nrow(pig60K),threshold.col=c('grey','black'),
       threshold.lty = c(1,2),threshold.lwd = c(1,1), amplify = T,
       signal.cex = c(1,1), signal.pch = c(20,20),signal.col = c("red","orange"))

绘制多性状曼哈顿图

CMplot(pig60K,plot.type = "m",threshold = c(0.01,0.05)/nrow(pig60K),threshold.col=c('grey','black'),
       threshold.lty = c(1,2),threshold.lwd = c(1,1), amplify = T, multracks = T,
       signal.cex = c(1,1), signal.pch = c(20,20),signal.col = c("red","orange"))

绘制环形曼哈顿图

CMplot(pig60K,plot.type="c",r=0.5,threshold=c(0.01,0.05)/nrow(pig60K),cex = 0.5, 
       threshold.col = c("red","orange"), threshold.lty = c(1,2),amplify = T, cir.chr.h = 2,
       signal.cex = c(2,2), signal.pch = c(19,20), signal.col=c("red","green"),outward=TRUE)

绘制单性状QQ图

CMplot(pig60K,plot.type = "q",threshold = 0.05)

绘制多性状QQ图

CMplot(pig60K,plot.type = "q",multracks = T, threshold = 0.05, threshold.col = "orange",
       amplify = T,signal.cex = 1.5, signal.pch = 20, signal.col = "red")