Plot positions of predicted retrotransposons along chromosomes

The positionas of LTR retrotransposons predicted with LTRpred will be visualized along the chromsome.

plot_element_distr_along_chromosome(
  pred,
  genome.file,
  centromere_start = NULL,
  centromere_end = NULL,
  ...
)

Arguments

pred	LTRpred.tbl generated with LTRpred.
genome.file	a file path to the genome assembly file in fasta format for which chromosomes shall be visualized.
centromere_start	a numeric vector storing the centromere start coordinates in the genome.file. The position in the numeric vector should correspond to the chromosome name in the genome.file fasta file. If centromere_start = NULL (default), then no centromeres will be drawn.
centromere_end	a numeric vector storing the centromere end coordinates in the genome.file. The position in the numeric vector should correspond to the chromosome name in the genome.file fasta file. If centromere_end = NULL (default), then no centromeres will be drawn.
...	additional arguments that shall be passed to the visualization function autoplot.

Author

Hajk-Georg Drost

Examples

if (FALSE) {
test_genome <- system.file("Hsapiens_ChrY.fa", package = "LTRpred")
test_pred <- LTRpred::read.ltrpred(
system.file("Hsapiens_ChrY_LTRpred_DataSheet.tsv", 
             package = "LTRpred"))
test_centromere_starts <- 55000
# generate visualization
LTRpred::plot_element_distr_along_chromosome(test_pred, test_genome, test_centromere_starts)
}