pSitePlot {ORFik} | R Documentation

## Plot area around TIS as histogram

### 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,
      type = "canonical CDS",
      scoring = "Averaged counts",
      forHeatmap = FALSE
    )

### 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 (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf.
`type` | character (canonical CDS), type for plot
`scoring` | character, default: (Averaged counts), which scoring did you use ? see ?coverageScorings for info and more alternatives.
`forHeatmap` | a logical (FALSE), should the plot be part of a heatmap? It will scale it differently. Removing title, x and y labels, and truncate spaces between bars.

### Details

The region is represented as a histogram with different colors for the 3 frames. To make it easy to see patterns in the reads. Remember if you want to change anything like colors, just return the ggplot object, and reassign like: obj + scale_color_brewer() etc.

### 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)
    pSitePlot(coverage)

    # See vignette for more examples

[Package ORFik version 1.10.13 Index]