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 = unique(hitMap$fraction),
      region = "start",
      output = NULL,
      type = "canonical CDS",
      scoring = "Averaged counts",
      forHeatmap = FALSE,
      title = "auto",
      facet = FALSE,
      frameSum = 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 read 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.
`title` | character, title of plot. Default "auto", will make it: paste("Length", length, "over", region, "of", type). Else set your own (set to NULL to remove all together).
`facet` | logical, default FALSE. If you input multiple read lengths, specified by fraction column of hitMap, it will split the plots for each read length, putting them under each other. Ignored if forHeatmap is TRUE.
`frameSum` | logical default FALSE. If TRUE, add an addition plot to the right, sum per frame over all positions per length.

### 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 1.12.13 Index]