Duplication rate ~ total read count plot

Description

duprateExpDensPlot Duplication rate ~ total read count plot

Usage

duprateExpDensPlot(DupMat, pal = c("cyan", "blue", "green", "yellow", "red"),
  tNoAlternative = TRUE, tRPKM = TRUE, tRPKMval = 0.5, tFit = TRUE,
  addLegend = TRUE, ...)

Arguments

Details

This function makes a scatter plot showing the per gene duplication rate versus the total read count.

Value

nothing

Examples

# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)

# duprate plot
duprateExpDensPlot(DupMat=dm)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(dupRadar)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dupRadar/duprateExpDensPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: duprateExpDensPlot
> ### Title: Duplication rate ~ total read count plot
> ### Aliases: duprateExpDensPlot
> 
> ### ** Examples
> 
> # dm is a duplication matrix calculated by analyzeDuprates:
> # R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
> attach(dupRadar_examples)
> 
> # duprate plot
> duprateExpDensPlot(DupMat=dm)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>