kmr_plot_map

Create a quick overview of the kmers mapped to a region around the given position.

kmr_plot_map(kmers, snp_pos)

Arguments

kmers	a GenomicRange object
snp_pos	a position on the sequence

Value

ggbio plot

See also

Other kmer_help: kmr_compare(), kmr_length_fasta(), kmr_map_kmers(), kmr_plot_response(), kmr_position_coverage(), kmr_response(), kmr_scan_k_min()

Examples

if (interactive()) {

  fa <- system.file("testdata/phix174.fasta", package = "kmerize")
  a <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
                   package = "kmerize")
  b <- system.file("testdata/phix174_m-pe_w_err_5k_30q.fastq.gz",
                   package = "kmerize")

  x <- kmr_scan_k_min(a, b, k = 9, min_kmers = 3, cleanup = FALSE)
  rr <- kmr_read_rds(x$kmer_tbl)


  kmap <- kmr_map_kmers(rr, genome = fa, "phi-X174")
  kmr_plot_map(kmap, snp_pos = 911)
}