transcriptWindow1: Meta coverage over all transcripts

In JokingHero/ORFik: Open Reading Frames in Genomics

Meta coverage over all transcripts

Description

Given as single window

Usage

transcriptWindow1(
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  colors = experiment.colors(df),
  title = "Coverage metaplot",
  windowSize = 100,
  returnPlot = is.null(outdir),
  dfr = NULL,
  idName = "",
  plot.ext = ".pdf",
  type = "ofst",
  drop.zero.dt = drop.zero.dt,
  BPPARAM = bpparam()
)

Arguments

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.
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: "default"), load files in experiment or some precomputed variant, like "ofst" or "pshifted". These are made with ORFik:::convertLibs(), shiftFootprintsByExperiment(), etc. Can also be custom user made folders inside the experiments bam folder. It acts in a recursive manner with priority: If you state "pshifted", but it does not exist, it checks "ofst". If no .ofst files, it uses "default", which always must exists. Presets are (folder is relative to default lib folder, some types fall back to other formats if folder does not exist): - "default": load the original files for experiment, usually bam. - "ofst": loads ofst files from the ofst folder, relative to lib folder (falls back to default) - "pshifted": loads ofst, wig or bigwig from pshifted folder (falls back to ofst, then default) - "cov": Load covRle objects from cov_RLE folder (fail if not found) - "covl": Load covRleList objects, from cov_RLE_List folder (fail if not found) - "bed": Load bed files, from bed folder (falls back to default) - Other formats must be loaded directly with fimport
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

See Also

Other experiment plots: transcriptWindow(), transcriptWindowPer()

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