RiboQC.plot {ORFik} | R Documentation

## Quality control for pshifted Ribo-seq data

### Description

Quality control for pshifted Ribo-seq data

### Usage

    RiboQC.plot(
      df,
      output.dir = file.path(dirname(df$filepath[1]), "QC_STATS/"),
      width = 6.6,
      height = 4.5,
      type = "pshifted",
      weight = "score",
      BPPARAM = BiocParallel::SerialParam(progressbar = TRUE)
    )

### Arguments

`df` | an ORFik `experiment`
`output.dir` | directory to save plot, default: file.path(dirname(df$filepath[1]), "QC_STATS/"). If NULL will not save.
`width` | width of plot, default 6.6 (in inches)
`height` | height of plot, default 4.5 (in inches)
`type` | type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths!
`weight` | which column in reads describe duplicates, default "score".
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`

### Value

ggplot object as a grid

### Examples

    df <- ORFik.template.experiment()
    df <- df[3,] #lets only p-shift RFP sample at index 3
    #shiftFootprintsByExperiment(df)
    #RiboQC.plot(df)

[Package ORFik version 1.10.13 Index]