DTEG.plot {ORFik} | R Documentation

## Plot DTEG result

### Description

For explanation of plot catagories, see `DTEG.analysis`

### Usage

    DTEG.plot(
      dt,
      output.dir = NULL,
      p.value = 0.05,
      plot.title = "",
      plot.ext = ".pdf",
      width = 6,
      height = 6,
      dot.size = 0.4,
      xlim = "bidir.max",
      ylim = "bidir.max",
      relative.name = paste0("DTEG_plot", plot.ext)
    )

### Arguments

`dt` | a data.table with the results from `DTEG.analysis`
`output.dir` | a character path, default NULL(no save), or a directory to save to a file. Relative name of file, specified by 'relative.name' argument.
`p.value` | a numeric, default 0.05 in interval (0,1) or "" to not show. What p-value used for the analysis? Will be shown as a caption.
`plot.title` | title for plots, usually name of experiment etc
`plot.ext` | character, default: ".pdf". Alternatives: ".png" or ".jpg".
`width` | numeric, default 6 (in inches)
`height` | numeric, default 6 (in inches)
`dot.size` | numeric, default 0.4, size of point dots in plot.
`xlim` | numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of rna column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max x limit: like c(-5, 5)
`ylim` | numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of rfp column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max y limit: like c(-10, 10)
`relative.name` | character, Default: `paste0("DTEG_plot", plot.ext)` Relative name of file to be saved in folder specified in output.dir. Change to .pdf if you want pdf file instead of png.

### Value

a ggplot object

### See Also

Other DifferentialExpression: `DEG.plot.static()`, `DTEG.analysis()`, `te.table()`, `te_rna.plot()`

### Examples

    df <- ORFik.template.experiment()
    df.rfp <- df[df$libtype == "RFP",]
    df.rna <- df[df$libtype == "RNA",]
    #dt <- DTEG.analysis(df.rfp, df.rna)
    #Default scaling
    #DTEG.plot(dt)
    #Manual scaling
    #DTEG.plot(dt, xlim = c(-2, 2), ylim = c(-2, 2))

[Package ORFik version 1.14.7 Index]