pSitePlot {ORFik} | R Documentation

## Plot area around TIS for p-shifted reads

### Description

Usefull to validate p-shifting is correct Can be used for any coverage of region around a point, like TIS, TSS, stop site etc.

### Usage

    pSitePlot(hitMap, length = 29, region = "start", output = NULL)

### Arguments

`hitMap` | a data.frame/data.table, given from metaWindow (must have columns: position, (score or count) and frame)
`length` | an integer (29), which length is this for?
`region` | a character (start), either "start or "stop"
`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.

### 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`, `savePlot`, `windowCoveragePlot`

### Examples

    # An ORF
    grl <- GRangesList(tx1 = GRanges("1", IRanges(1, 6), "+"))
    # Ribo-seq reads
    range <- IRanges(c(rep(1, 3), 2, 3, rep(4, 2), 5, 6), width = 1 )
    reads <- GRanges("1", range, "+")
    coverage <- coveragePerTiling(grl, reads, TRUE, as.data.table = TRUE,
                                  withFrames = TRUE)
    ORFik:::pSitePlot(coverage)

    # See vignette for more examples

[Package ORFik version 1.4.1 Index]