te_rna.plot {ORFik} | R Documentation

## Translational efficiency plots

### Description

Create TE plot of:
- Within sample (TE log2 vs mRNA fpkm)

### Usage

    te_rna.plot(
      dt,
      output.dir = NULL,
      filter.rfp = 1,
      filter.rna = 1,
      plot.title = "",
      plot.ext = ".pdf",
      width = 6,
      height = "auto",
      dot.size = 0.4,
      xlim = c(filter.rna, filter.rna + 2.5)
    )

### Arguments

`dt` | a data.table with the results from `te.table`
`output.dir` | a character path, default NULL(no save), or a directory to save to a file will be called "TE_within.pdf"
`filter.rfp` | numeric, default 1. What is the minimum fpkm value?
`filter.rna` | numeric, default 1. What is the minimum fpkm value?
`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` | a numeric, width of plot in inches. Default "auto".
`dot.size` | numeric, default 0.4, size of point dots in plot.
`xlim` | numeric vector of length 2. X-axis limits. Default: `c(filter.rna, filter.rna + 2.5)`

### Value

a ggplot object

### See Also

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

### Examples

    df <- ORFik.template.experiment()
    df.rfp <- df[df$libtype == "RFP",]
    df.rna <- df[df$libtype == "RNA",]
    #dt <- te.table(df.rfp, df.rna)
    #te_rna.plot(dt, filter.rfp = 0, filter.rna = 5, dot.size = 1)

[Package ORFik version 1.14.7 Index]