eventPlot: eventPlot

In dianalow/SPLINTER: Splice Interpreter of Transcripts

eventPlot

Description

eventPlot

Usage

eventPlot(
  transcripts,
  roi_plot = NULL,
  bams = c(),
  names = c(),
  annoLabel = c("Gene A"),
  rspan = 1000,
  pfam_dom = NULL,
  showAll = TRUE
)

Arguments

transcripts	GRanges object
roi_plot	GRanges object region to plot
bams	character vector of bam file locations
names	character vector of name labels
annoLabel	character. annotation label
rspan	integer or NULL. number of basepairs to span from roi. if NULL, will consider whole gene of roi
pfam_dom	optional GRanges object of PFAM domains from UCSC Tables.
showAll	logical. TRUE = display splice junctions of entire view or FALSE = just roi.

Value

a Gviz plot of genomic region

Author(s)

Diana Low

Examples

# define BAM files
data_path<-system.file("extdata",package="SPLINTER")
mt<-paste(data_path,"/mt_chr14.bam",sep="")
wt<-paste(data_path,"/wt_chr14.bam",sep="")

# plot results
eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt),
 names=c('wt','mt'),rspan=1000)

dianalow/SPLINTER documentation built on March 28, 2024, 2:07 p.m.