plotHelper: Helper function for coverage plots

In Roleren/ORFik: Open Reading Frames in Genomics

Helper function for coverage plots

Description

Should only be used internally

Usage

plotHelper(
  coverage,
  df,
  outdir,
  scores,
  returnCoverage = FALSE,
  title = "coverage metaplot",
  plot.ext = ".pdf",
  colors = c("skyblue4", "orange"),
  plotFunction = "windowCoveragePlot"
)

Arguments

coverage	a data.table containing at least columns (count/score, position), it is possible to have additionals: (genes, fraction, feature)
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.
returnCoverage	(defualt: FALSE), return the ggplot object (TRUE) or NULL (FALSE).
title	Title to give plot
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg".
colors	Which colors to use, default auto color from function experiment.colors, new color per library type. Else assign colors yourself.
plotFunction	Which plot function, default: windowCoveragePlot

Value

NULL (or ggplot object if returnCoverage is TRUE)

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.