Function reference • pafr

Reading files into R Functions for reading aligments and genomic intervals
`read_paf()`	Read a genomic alignment in PAF format
`read_bed()`	Read genomic intervals in bed format
`as_paf()`	Coerce a data.frame or tibble into a pafr object
Plotting alignments Functions to produce ggplot visualisations of genome-aligments
`dotplot()`	Generate a dot plot from a paf alignment
`plot_coverage()`	Plot the regions of one genome that are covered by alignments in a paf file
`plot_synteny()`	Plot synteny between a query and target sequence in a PAF alignment
`highlight_query()` `highlight_target()`	Highlight segments of a query or target genome in a dot plot
`theme_coverage_plot()`	A minimalistic ggplot2 theme designed for use with genome coverage plots
`Gb_lab()` `Mb_lab()` `Kb_lab()`	Number formatters for scales in base pairs
Utility functions Helper functions
`filter_secondary_alignments()`	Remove secondary alignments from a pafr alignment
`chrom_sizes()`	Extract the sizes of all sequences in a paf alignment

Reference