transcriptWindow: Make 100 bases size meta window for all libraries in...
In Roleren/ORFik: Open Reading Frames in Genomics

transcriptWindow

R Documentation

Make 100 bases size meta window for all libraries in experiment

Description

Gives you binned meta coverage plots, either saved seperatly or all in one.

Usage

transcriptWindow(
  leaders,
  cds,
  trailers,
  df,
  outdir = NULL,
  scores = c("sum", "transcriptNormalized"),
  allTogether = TRUE,
  colors = experiment.colors(df),
  title = "Coverage metaplot",
  windowSize = min(100, min(widthPerGroup(leaders, FALSE)), min(widthPerGroup(cds,
    FALSE)), min(widthPerGroup(trailers, FALSE))),
  returnPlot = is.null(outdir),
  dfr = NULL,
  idName = "",
  plot.ext = ".pdf",
  type = "ofst",
  is.sorted = FALSE,
  drop.zero.dt = TRUE,
  BPPARAM = bpparam()
)

Arguments

`leaders`	a `GRangesList` of leaders (5' UTRs)
`cds`	a `GRangesList` of coding sequences
`trailers`	a `GRangesList` of trailers (3' UTRs)
`df`	an ORFik `experiment`
`outdir`	directory to save to (default: NULL, no saving)
`scores`	scoring function (default: c("sum", "transcriptNormalized")), see ?coverageScorings for possible scores.
`allTogether`	plot all coverage plots in 1 output? (defualt: TRUE)
`colors`	Which colors to use, default auto color from function `experiment.colors`, new color per library type. Else assign colors yourself.
`title`	title of ggplot
`windowSize`	size of binned windows, default: 100
`returnPlot`	return plot from function, default is.null(outdir), so TRUE if outdir is not defined.
`dfr`	an ORFik `experiment` of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.
`idName`	A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "")
`plot.ext`	character, default: ".pdf". Alternatives: ".png" or ".jpg".
`type`	a character(default: "ofst"), load files in experiment or some precomputed variant, either "ofst", "pshifted" or "default". These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found
`is.sorted`	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`drop.zero.dt`	logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently)
`BPPARAM`	how many cores/threads to use? default: bpparam()

Value

NULL, or ggplot object if returnPlot is TRUE

Examples

df <- ORFik.template.experiment()[3,] # Only third library
loadRegions(df) # Load leader, cds and trailers as GRangesList
#transcriptWindow(leaders, cds, trailers, df, outdir = "directory/to/save")

Roleren/ORFik documentation built on April 25, 2024, 8:41 p.m.