windowCoveragePlot {ORFik} | R Documentation

## Get coverage window plot of reads

### Description

Spanning a region like a transcripts, plot how the reads distribute.

### Usage

    windowCoveragePlot(coverage, output = NULL, scoring = "zscore",
      colors = c("skyblue4", "orange"), title = "Coverage metaplot",
      type = "transcript")

### Arguments

`coverage` | a data.table, output of scaledWindowCoverage
`output` | character string (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf.
`scoring` | character vector (zscore), either of zScore, transcriptNormalized, sum, mean, median, NULL. Set NULL if already scored.
`colors` | character vector colors to use in plot
`title` | a character (metaplot) (what is the title of plot?)
`type` | a character (transcript), what should legends say is the whole region? Transcript, gene, non coding rna etc.

### Details

If you return this function without assigning it and output is NULL, it will automaticly plot the figure in your session. If output is assigned, no plot will be shown in session.

### Value

a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.

### See Also

Other coveragePlot: `coverageHeatMap`, `pSitePlot`, `savePlot`

### Examples

    library(data.table)
    coverage <- data.table(position = seq(20), score = cumsum(seq(20)))
    windowCoveragePlot(coverage)
    # See vignette for a more practical example

[Package ORFik version 1.4.1 Index]