transcriptWindow1 {ORFik}R Documentation

Meta coverage over all transcripts

Description

Given as single window

Usage

transcriptWindow1(
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  colors = rep("skyblue4", nrow(df)),
  title = "Coverage metaplot",
  windowSize = 100,
  returnPlot = is.null(outdir),
  dfr = NULL,
  idName = "",
  format = ".png",
  type = "ofst",
  BPPARAM = bpparam()
)

Arguments

df

an ORFik experiment

outdir

directory to save to (default: NULL, no saving)

scores

scoring function (default: c("sum", "zscore")), see ?coverageScorings for possible scores.

colors

Which colors to use, default (skyblue4)

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: "")

format

default (".png"), do ".pdf" if you want as pdf

type

a character(default: "bedoc"), load files in experiment or some precomputed variant, either "bedo", "bedoc", "pshifted" or default. These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found

BPPARAM

how many cores/threads to use? default: bpparam()

Value

NULL, or ggplot object if returnPlot is TRUE

See Also

Other experiment plots: transcriptWindowPer(), transcriptWindow()


[Package ORFik version 1.8.6 Index]