windowCoveragePlot: Get meta coverage plot of reads

In JokingHero/ORFik: Open Reading Frames in Genomics

Get meta coverage 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 = "transcripts",
  scaleEqual = FALSE,
  setMinToZero = FALSE
)

Arguments

coverage	a data.table, e.g. 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, default "zscore", either of zscore, transcriptNormalized, sum, mean, median, .. or NULL. Set NULL if already scored. see ?coverageScorings for info and more alternatives.
colors	character vector colors to use in plot, will fix automaticly, using binary splits with colors c('skyblue4', 'orange').
title	a character (metaplot) (what is the title of plot?)
type	a character (transcripts), what should legends say is the whole region? Transcripts, genes, non coding rnas etc.
scaleEqual	a logical (FALSE), should all fractions (rows), have same max value, for easy comparison of max values if needed.
setMinToZero	a logical (FALSE), should minimum y-value be 0 (TRUE). With FALSE minimum value is minimum score at any position. This parameter overrides scaleEqual.

Details

If coverage has a column called feature, this can be used to subdivide the meta coverage into parts as (5' UTRs, cds, 3' UTRs) These are the columns in the plot. The fraction column divide sequence libraries. Like ribo-seq and rna-seq. These are the rows of the plot. 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. NULL is returned and object is saved to output.

Colors: 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(), pSitePlot(), savePlot()

Examples

library(data.table)
coverage <- data.table(position = seq(20),
                       score = sample(seq(20), 20, replace = TRUE))
windowCoveragePlot(coverage)

#Multiple plots in one frame:
coverage2 <- copy(coverage)
coverage$fraction <- "Ribo-seq"
coverage2$fraction <- "RNA-seq"
dt <- rbindlist(list(coverage, coverage2))
windowCoveragePlot(dt, scoring = "log10sum")

# See vignette for a more practical example

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