# plotCNVHeatmap_genome

**Repository Path**: chens1209/plotCNVHeatmap_genome

## Basic Information

- **Project Name**: plotCNVHeatmap_genome
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-08-11
- **Last Updated**: 2020-12-20

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


#改写R 包 copynumber 里面的plotHeatmap函数，实现以下效果
![CNV热图](https://github.com/wangweifeng2018/plotCNVHeatmap_genome/blob/master/CNV_heatmap.png)

#Step1. 下载 Bioconductor-copynumber 源码文件，
-----------------
```
$wget http://www.bioconductor.org/packages/release/bioc/src/contrib/copynumber_1.26.0.tar.gz
$tar -zxvf copynumber_1.26.0.tar.gz
$cd copynumber/R/
```
#Step2.修改源码文件
-----------------
##修改addChromlines.r文件在底部添加染色体信息
-----------------
(1) 源码只支持去掉Y染色体展示，不支持X,Y同时去掉.更改 Row 41-46为如下，使之支持X,Y都不展示,并重新定义chrom.names。
 ```
 if(any(chromosomes==24)){
                         chromosomes <- 1:24
                         chrom.names <- c(1:22,"X","Y")
                        }else{
                                if(any(chromosomes==23)){
                                chromosomes <- 1:23
                                chrom.names <- c(1:22,"X")
                                chrom.mark <- chrom.mark[-length(chrom.mark)]
                                }else{
                                chromosomes <- 1:22
                                chrom.names <- 1:22
                                chrom.mark <- chrom.mark[-length(chrom.mark)]
                                chrom.mark <- chrom.mark[-length(chrom.mark)]
                                }   
                        }  
 ```
(2)注释掉Row 65，使用上述定义的chrom.name
```
#chrom.names <- unique(chromosomes)
```
(3)注释掉 row 67-69，将所有染色体标签移到热图下方。
```
        #Plot half at bottom, half at top:
        #bot <- seq(1,length(chrom.mark),2)
        #top <- seq(2,length(chrom.mark),2)
        #mtext(chrom.names[bot],side=1,line=arg$chrom.line[1],at=at[bot],cex=arg$chrom.cex)
        text(x = at[seq(length(chrom.mark))-0.5],y=rep(-3,length(chrom.mark)),labels=chrom.names,pos=1,cex=arg$chrom.cex)
 ```
 (4)row 70 后面紧接着添加如下代码，在热图绘制染色体条带。
 ```
        # plot chromosome strip at the bottom of the figure
        xleft <- chrom.mark[1:(length(chrom.mark)-1)]
        xright <- chrom.mark[2:(length(chrom.mark))]
        par(col = "black",bty="n")
        rect(xleft,c(rep(-3,length(chrom.mark)-1)),xright,c(rep(0,length(chrom.mark)-1)),col = rep(c("black","white"),length(chrom.mark)-1))
 ```
 
##修改 plotHeatmap.r 文件添加Legend
------------
在Row 181 后面添加如下代码
```
    # Legend
    colfunc <- colorRampPalette(c("dodgerblue", "white","red"))
    rect(c(300:800),rep(-13,500),c(301:801),rep(-10,500),col=colfunc(500),cex=1,border=NA)
    text(x=c(300,550,800),y=rep(-14,3),pos=1,labels=c(lower.lim,0,upper.lim),cex=1)
```

#Step3. 使用修改后脚本绘图
-----------
（1）load 参考文件等
```
load("yourdir_path/R/sysdata.rda")
```
（2）source 修改后R脚本
```
for (f in list.files(path="youdir_path/R/",pattern="*.r$")){
        source_f = paste("yourdir_path/",f,sep = "") 
        source(source_f)
}
```
(3) plot
```
png(paste($your_outdir,"CNV_heatmap.png",sep = "/"),width=4000,height=3000,res=400)
plotHeatmap(segments=seg,lower.lim=-0.5
                ,upper.lim=0.5
                ,sample.labels=F
                ,xaxis="pos"
                ,colors=c("dodgerblue","white","red"))
dev.off()
```