ggRearrange: ggplot wrapper for plotting reads supporting a rearrangement

In cancer-genomics/trellis: Somatic structural variant analysis

ggplot wrapper for plotting reads supporting a rearrangement

Description

ggplot wrapper for plotting reads supporting a rearrangement

Usage

ggRearrange(df, ylab = "Read pair index", basepairs = 400, num.ticks = 5)

Arguments

df	a data.frame as created by rearDataFrame
ylab	y-axis label
basepairs	integer specifying size of window in basepairs
num.ticks	integer specifying number of x-axis ticks

See Also

rearDataFrame

Examples

  data(rlist)
  extdata <- system.file("extdata", package="svbams")
  unmap.file <- file.path(extdata, "blat_unmapped.txt")
  blat_unmap <- readBlat(unmap.file)
  split_reads <- rearrangedReads(linkedBins(rlist),
                                 blat_unmap, 500)
  splitReads(rlist) <- split_reads
  rlist2 <- fiveTo3List(rlist, build="hg19")
  r <- rlist2[[1]]
  df <- rearDataFrame(r, "hg19")
  ## Not run: 
    ggRearrange(df)
  
## End(Not run)

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.