pSitePlot: Plot area around TIS as histogram

In JokingHero/ORFik: Open Reading Frames in Genomics

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

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.