mmextract: Extract all scaffolds within a selection polygon
In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description Usage Arguments Value Author(s) Examples

Finds all scaffolds that fall into a selection polygon highlighted in a plot generated by mmplot.

1	mmextract(mm, selection, min_length = 0, inverse = FALSE)

`mm`	(required) A dataframe loaded with `mmload`.
`selection`	(required) A 2-column dataframe with the x and y coordinates of a selection of points in an `mmplot`. The column names of the provided dataframe must match column names in `mm`.
`min_length`	Filter all scaffolds with a length at or below this value before the extraction. (Default: `0`)
`inverse`	(Logical) If `TRUE`, then the scaffolds within the `selection` are instead removed. (Default: `FALSE`)

A dataframe (tibble) compatible with other mmgenome2 functions.

Kasper Skytte Andersen ksa@bio.aau.dk

Soren M. Karst smk@bio.aau.dk

Mads Albertsen MadsAlbertsen85@gmail.com

library(mmgenome2)
data(mmgenome2)
mmgenome2
selection <- data.frame(
  cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
  cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2,
  min_length = 3000,
  selection = selection,
  inverse = FALSE
)
mmgenome2_extraction