plotCNA：增加CNV的绘图功能

[qingjian1991]

我对plotCNA的代码进行了修改，增加了3个函数参数。

对应的修改后的脚本在这个文件中。
plotCNA.txt

Type.name：指定用于绘图的列
Type.colors：指定对应的颜色
rect.patients.size：按照病人加一个长方形的框区分病人

我们在绘制CNV时，可能想自己定义CNV的类型和对应的颜色表示

# read data
segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit")
seg <- readSegment(segFile = segFile)

# define the new columns
# 0-6 copy numbers, add cnLOH, LOH >=2 copys
Copy_cutoff = function(seg){
  seg %>%
    mutate(CopyNumber1 = ifelse(CopyNumber >5, 6, CopyNumber) ) %>%
    mutate(CopyNumber1 = ifelse(CopyNumber == 2 & Minor_CN == 0, "cnLOH",  CopyNumber1)) 
}

seg1 = lapply(seg, Copy_cutoff)

用原始的程序绘图

#original plot
plotCNA(seg1,
         showRownames = FALSE)

重新定于拷贝数的情况及其颜色

plotCNA(seg1,
         Type.name = "CopyNumber1",
         Type.colors = setNames(
           c("#7D8BCD", "#B1B9E7", "#F6F7F7", "#E4A8B5", "#CB7185","#B03D5E","#99143C", "#91BAA7"), 
           nm = c(seq(0,6), "cnLOH")
         ),
         showRownames = FALSE,
         rect.patients.size = 0
         
)

绘制minor-copy的情况

#Plot Minor_CNVs
plotCNA(seg1,
         Type.name = "Minor_CN",
         Type.colors = setNames(
           c("#7D8BCD", "#F6F7F7", "#E4A8B5", "#CB7185","#B03D5E"), 
           nm = 0:4
         ),
         showRownames = FALSE,
         rect.patients.size = 0
)

绘制minor-copy的情况并对每一个病人加一个长方形的框表示病人

#Plot Minor_CNVs and add a rectangle to indicate the patients
plotCNA(seg1,
         Type.name = "Minor_CN",
         Type.colors = setNames(
           c("#7D8BCD", "#F6F7F7", "#E4A8B5", "#CB7185","#B03D5E"), 
           nm = 0:4
         ),
         showRownames = FALSE,
         rect.patients.size = 0.3
)

[likelet]

@Niinleslie update the code accordingly, Many thanks for your improvement to our code @qingjian1991