kmr_plot_response: kmr_plot_response
In c5sire/kmerize: K-Mer Tools for Building Databases

Description Usage Arguments Value See Also Examples

Plots genomics response object.

1	kmr_plot_response(res, ref_k = NULL, limit = 0, max_y = -1)

`res`	result from genomic response scan
`ref_k`	a reference k value to include
`limit`	a numeric value between 0 and 1. If 0 no line will be displayed. Default is 0. A recommended value is 0.95.
`max_y`	a maximum y value. Default 0 indicates automatic selection.

plot

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

if (interactive()) {
  fa <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
    package = "kmerize"
  )
  fp <- system.file("testdata/phix174.fasta", 
                     package = "kmerize")
  dna <- Biostrings::readDNAStringSet(fp)

  k <- as.integer(seq(3, 17, 2))


  res <- kmr_response(fa, k, fmt = "q")
  kmr_plot_response(res, ref_k = 9, max_y = max(res$distinct))
}