PLOTch3: PLOTch3
In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

PLOTch3

R Documentation

PLOTch3

Description

plot 2 sets of RNA-seq and ribo-seq for comparison. It also contains a plot with transcript models.

Usage

PLOTch3(
  YFG,
  RNAbam1 = RNAseqBam1,
  ribo1 = Ribo1,
  Deg = DEGdata,
  CAGE = CAGEdata,
  SAMPLE1 = S_NAME1,
  SAMPLE2 = S_NAME2,
  SAMPLE3 = S_NAME3,
  CDSonly = FALSE,
  Extend = 50,
  isoform,
  uORF = NULL,
  NAME = "",
  uORFisoform,
  GREY = c(FALSE, TRUE, TRUE)
)

Arguments

`YFG`	Gene ID
`RNAbam1`	Dataset 1 to plot. Default is RNAseqBam1 that was loaded by rna_bam.ribo.
`ribo1`	riboseq dataset 1
`SAMPLE1`	name of sample 3
`CDSonly`	TRUE or FALSE. Only plot CDS region or all riboseq reads in defined area. Default plot all riboseq reads in the defined area.
`Extend`	Integer. The number of extra nt ploted at the ends of the plots.
`isoform`	Integer. Which isoform to plot periodicity.
`uORF`	Gene ID for uORF
`NAME`	Name of the gene
`uORFisoform`	Isoform number of the uORF
`GREY`	grey color or three colors for Ribo/Degradome/CAGE