下载参考基因组

下载地址：


wget http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

wget http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz

#不能使用压缩格式的基因组和注释，先解压

gunzip Mus_musculus.GRCm38.102.gtf.gz Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

参考链接：https://www.jianshu.com/p/ca6aada5cbf1

分组


install.packages("devtools")

devtools::install_github("dzhang32/ggtranscript")

library("ggtranscript")
devtools::install_github('junjunlab/tackPlotR')

library(tackPlotR)

library(ggsci)

library(rtracklayer)

# 1.load gtf读取 bigwig 文件 

gtf <- import.gff('Mus_musculus.GRCm38.102.gtf') %>%

  data.frame()

# help

?loadBWfile

file <- c(

  "control.input.bw", "control.ip.bw",

  "t1.input.bw", "t1.ip.bw",

  "t2.input.bw", "t2.ip.bw"

)

samp <- c(

  "control.input", "control.ip",

  "t1.input", "t1.ip",

  "t2.input", "t2.ip"

)

group1 <- c(rep(c("Input", "IP"), 3))

group2 <- c(rep("Control", 2), rep("T1", 2), rep("T2", 2))

# 2.load bw files

allBw <- loadBWfile(file = file, sample = samp, group1 = group1, group2 = group2)

# check

head(allBw,3)

#  seqnames  start    end  score        sample group1  group2

# 1        1      1 3001485  0.0000 control.input  Input Control

# 2        1 3001486 3001490 12.5599 control.input  Input Control

# 3        1 3001491 3001510 25.1199 control.input  Input Control
#基本绘图:。
plotTrack(

  gtfFile = gtf,

  gene = "Actb",

  arrowCol = "black",

  bigwigFile = allBw,

  sampleAes = "group1",

  facetVars = "sample"

)

image

修改映射变量:

plotTrack(
  gtfFile = gtf,
  gene = "Actb",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "sample",
  facetVars = "sample"
)

image.png

修改 track 颜色:

plotTrack(
  gtfFile = gtf,
  gene = "Actb",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "sample",
  facetVars = "sample",
  trackCol = pal_lancet()(6)
)

image.png

绘制多个转录本结构, 默认绘制 CDS 和 exon 最长的转录本:

plotTrack(
  gtfFile = gtf,
  gene = "Tnf",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "group1",
  facetVars = "sample",
  multiple = TRUE,
  myTransId = c("ENSMUST00000025263", "ENSMUST00000167924")
)

image.png

修改分面填充颜色:

plotTrack(
  gtfFile = gtf,
  gene = "Actb",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "group1",
  addfacetCol = TRUE,
  facetVars = "sample",
  facetFill = pal_d3()(6),
  borderCol = rep("white", 6)
)

image.png

添加分面:

plotTrack(
  gtfFile = gtf,
  gene = "Actb",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "group1",
  facetVars = c("group2", "group1"),
  addfacetCol = TRUE,
  facetFill = c(pal_d3()(3), pal_npg()(6)),
  borderCol = rep("white", 9)
)

image.png

添加多层封面:

# add more one facet
plotTrack(
  gtfFile = gtf,
  gene = "Actb",
  arrowCol = "black",
  bigwigFile = allBw,
  sampleAes = "group1",
  facetVars = c("group2", "group1", "sample"),
  addfacetCol = TRUE,
  facetFill = c(pal_d3()(3), pal_npg()(6), pal_locuszoom()(6)),
  borderCol = rep("white", 15)
)

image.png