mmscanbins: Retrieve scaffold names from all genome bins in a folder
In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description Usage Arguments Value Examples

Reads all FASTA files (genome bins) in a folder and returns all unique scaffold names. This is useful to get an overview of which scaffolds are already extracted from the metagenome by for example highlighting them in plots.

1	mmscanbins(binfolder, namesOnly = TRUE)

`binfolder`	(required) Path to the folder to scan.
`namesOnly`	Return only the scaffold names (`TRUE`) or a complete list with the DNA sequences of the scaffolds in each file (`FALSE`). (Default: `TRUE`)

A character vector (if namesOnly = TRUE) or a list (if namesOnly = FALSE).

## Not run: 
# Use mmextract and mmexport to extract scaffolds from the assembly and
# write their sequences to a FASTA file per bin. Then the mmscanbins() function
# can be used to retrieve the names of all scaffolds already extracted, and
# then for example highlight them in a plot:

binned_scaffolds <- mmscanbins("path/to/folder", namesOnly = TRUE)
binned_scaffolds
mmplot(mmgenome2,
  min_length = 10000,
  x = "cov_C13.11.25",
  y = "cov_C14.01.09",
  color_by = "taxonomy",
  highlight_scaffolds = binned_scaffolds,
  highlight_color = "darkred",
  x_scale = "log10",
  y_scale = "log10"
)

## End(Not run)