smudgeplot plot

The algorithm to generate smudgeplot. This is just a wrapper around smudgeplot_plot.R, so if you preferred the 0.1.? interface, you can directly call smudgeplot_plot.R script. To see the help page, run it with --help flag.

Usage

usage: smudgeplot.py plot [-h] [-o O] [-q Q] [-L L] [-n N] [-t TITLE]
                          [-nbins NBINS] [-k K] [--homozygous]
                          [infile]

Generate 2d histogram for smudgeplot

positional arguments:
  infile                name of the input tsv file with covarages (default
                        "coverages_2.tsv")."

optional arguments:
  -h, --help            show this help message and exit
  -o O                  The pattern used to name the output (smudgeplot).
  -q Q                  Remove kmer pairs with coverage over the specified
                        quantile; (default none).
  -L L                  The lower boundary used when dumping kmers (default
                        min(total_pair_cov) / 2).
  -n N                  The expected haploid coverage (default estimated from
                        data).
  -t TITLE, --title TITLE
                        name printed at the top of the smudgeplot (default
                        none).
  -nbins NBINS          The number of nbins used for smudgeplot matrix (nbins
                        x nbins) (default autodetection).
  -k K                  The length of the kmer.
  --homozygous          Assume no heterozygosity in the genome - plotting a
                        paralog structure; (default False).