使用 Gviz 包由bam文件画比对峰图(AlignmentsTrack)

CentOS7 + R4.1.1 + Gviz1.36.2

1. 输入为10x bam 文件(CellRanger比对)

能整合 UCSC或ENSEMBL等来源的公开基因组注释数据

染色体必须以 chr 字符串开头，可以决定通过调用 options(ucscChromosomeNames=FALSE) 来关此功能

library(Gviz)

## for 10x
options(ucscChromosomeNames=FALSE) #10x没有这一行，就没有峰图

rnaTrack1 <- AlignmentsTrack( "/home/wangjl/data/bams/N5_NH_CB_list_filtered_c1.bam",
                              col.title="black", #左侧标题颜色
                              #showAxis=F,
                             isPaired = TRUE, name="cluster1")
rnaTrack1
rnaTrack5 <- AlignmentsTrack( "/home/wangjl/data/bams/N5_NH_CB_list_filtered_c5.bam",
                              col.title="black", #左侧标题颜色
                           isPaired = TRUE, name="cluster5")
bmt <- BiomartGeneRegionTrack(genome = "hg38", chromosome = "12",
                              start = 6534514, end = 6534514 + 10000,
                              # filter = list(with_ox_refseq_mrna = TRUE),
                              name="CTLA4",
                              col.title="red", #左侧标题颜色
                              stacking = "pack") #pack/dense

#plotTracks(list(rnaTrack1, bmt), #type="coverage", coverageHeight = 0.8)

plotTracks(c(rnaTrack1, rnaTrack5, bmt), type="coverage",
           main="10x dataset",
           from = 203873844-3000, to = 203873844 + 500, chromosome = "2",
           sizes = c(3,3,1))
#

图如下：

 

######### for other genes
# CCR7
bmt <- BiomartGeneRegionTrack(genome = "hg38", chromosome = "17",
                              start = 40558899, end = 40558899 + 10000,
                              # filter = list(with_ox_refseq_mrna = TRUE),
                              name="CCR7",
                              col.title="red", #左侧标题颜色
                              stacking = "pack") #pack/dense
plotTracks(c(rnaTrack1, rnaTrack5, bmt), type="coverage",
           main="10x dataset",
           from = 40558899-10000, to = 40558899 + 8500, chromosome = "17",
           sizes = c(3,3,1))
# GZMA
bmt <- BiomartGeneRegionTrack(genome = "hg38", chromosome = "5",
                              start = 55110133, end = 55110133 + 10000,
                              # filter = list(with_ox_refseq_mrna = TRUE),
                              name="GZMA",
                              col.title="red", #左侧标题颜色
                              stacking = "pack") #pack/dense
plotTracks(c(rnaTrack1, rnaTrack5, bmt), type="coverage",
           main="10x dataset",
           from = 55110133-8000, to = 55110133 + 500, chromosome = "5",
           sizes = c(3,3,1))

图略。

2. 输入为c1 bam 文件（STAR 比对）

library(Gviz)

rnaTrack1 <- AlignmentsTrack( "/home/wangjl/igv/GRB10/c01ROW31_GRB10.bam",
                              col.title="black", #左侧标题颜色
                              #showAxis=F,
                              isPaired = TRUE, name="c01ROW31")
rnaTrack1
rnaTrack5 <- AlignmentsTrack( "/home/wangjl/igv/GRB10/c15ROW22_GRB10.bam",
                              col.title="black", #左侧标题颜色
                              isPaired = TRUE, name="c15ROW22")
bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr7",
                              start = 50657767, end = 50657767 + 10000,
                              # filter = list(with_ox_refseq_mrna = TRUE),
                              name="GRB10",
                              col.title="red", #左侧标题颜色
                              stacking = "pack") #pack/dense

plotTracks(c(rnaTrack1, rnaTrack5, bmt), type="coverage",
           main="C1 dataset",
           from = 50657767-500, to = 50657767 + 3000, chromosome = "chr7",
           sizes = c(3,3,1))

 

# learn Gviz

官网文档: The Gviz User Guide 
# https://mp.weixin.qq.com/s?__biz=Mzg5MzYzNTcwNQ==&mid=2247490523&idx=1&sn=4d54c2e0f561c8d6eff88db8e9769928