gridPlotAssemblyVersions: Plot retrotransposon age distributions for predictions of...

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Plot retrotransposon age distributions for predictions of different genome assembly versions

Description

Compare the abundance of retrotransposon predictions between different genome assembly versions. This way a genome assembly version bias can be either ruled out or considered for subsequent conclusions.

Usage

gridPlotAssemblyVersions(
  data,
  quality.filter = FALSE,
  text.size = 18,
  xlab = "LTR similarity",
  ylab = "LTR retrotransposon count",
  main.text = "",
  y.ticks = 6,
  sim = 70,
  n.orfs = 0
)

Arguments

data	prediction files returned by LTRpred. Usually a combined prediction file that was generated with combinePreds.
quality.filter	shall false positives be filtered out as much as possible or not.
text.size	size of x-axis, y-axis, and title text.
xlab	x-axis label.
ylab	y-axis label.
main.text	title text.
y.ticks	number of ticks that shall be drawn on the y-axis.
sim	If quality.filter = TRUE: LTR similarity threshold. Only putative LTR transposons that fulfill this LTR similarity threshold will be retained.
n.orfs	If quality.filter = TRUE: minimum number of ORFs detected in the putative LTR transposon.

Author(s)

Hajk-Georg Drost

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.