Duplication rate ~ total read count plot — duprateExpDensPlot • dupRadar

duprateExpDensPlot Duplication rate ~ total read count plot

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

Arguments

DupMat: The duplication matrix calculated by analyzeDuprates
pal: The color palette to use to display the density
tNoAlternative: Display threshold of 1000 reads per kilobase
tRPKM: Display threshold at a given RPKM level
tRPKMval: The given RPKM level
tFit: Whether to fit the model
addLegend: Whether to add a legend to the plot
...: Other parameters sent to plot()

Value

nothing

Details

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

Examples

# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)
#> The following objects are masked from dupRadar_examples (pos = 3):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 4):
#> 
#>     dm, dm.bad

# duprate plot
duprateExpDensPlot(DupMat=dm)