correlation.plots {ORFik} | R Documentation

## Correlation plots between all samples

### Description

Get 3 correlation plots (1 simple (correlation colors), 2 complex with correlation value + dot plots of per gene ) of raw counts and log2(count + 1) over selected region in: c("mrna", "leaders", "cds", "trailers")

### Usage

    correlation.plots(
      df,
      output.dir,
      region = "mrna",
      type = "fpkm",
      height = 400,
      width = 400,
      size = 0.15,
      plot.ext = ".pdf",
      complex.correlation.plots = TRUE,
      data_for_pairs = countTable(df, region, type = type)
    )

### Arguments

`df` | an ORFik `experiment`
`output.dir` | directory to save to, 2 files named: cor_plot.pdf and cor_plot_log2.pdf
`region` | a character (default: mrna), make raw count matrices of whole mrnas or one of (leaders, cds, trailers)
`type` | which value to use, "fpkm", alternative "counts".
`height` | numeric, default 400 (in mm)
`width` | numeric, default 400 (in mm)
`size` | numeric, size of dots, default 0.15.
`plot.ext` | character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!
`complex.correlation.plots` | logical, default TRUE. Add in addition to simple correlation plot two computationally heavy dots + correlation plots. Useful for deeper analysis, but takes longer time to run, especially on low-quality gpu computers. Set to FALSE to skip these.
`data_for_pairs` | a data.table from ORFik::countTable of counts wanted. Default is fpkm of all mRNA counts over all libraries.

### Value

invisible(NULL)

[Package ORFik version 1.12.13 Index]