Plot retrotransposon age distributions for predictions of different genome assembly versions

Source: R/gridPlotAssemblyVersions.R

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.

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

Hajk-Georg Drost