Remove bins from a strollur object

Designed with package integration in mind, the remove bins function allows you to remove bins from a strollur object

Usage

xdev_remove_bins(data, bin_names, trash_tags, bin_type = "otu")

Arguments

data

a strollur object.

bin_names

a vector of strings containing the names of the bins you would like removed.

trash_tags

a vector of strings containing the reasons you are removing each bin

bin_type

a string indicating the type of clusters.

Value

an updated strollur object

Examples

  data <- strollur::new_dataset(dataset_name = "my_dataset")

  bin_names <- c("bin1", "bin2", "bin3")
  abundances <- c(110, 525, 80)

  strollur::xdev_assign_bins(data,
                   table = data.frame(bin_name = bin_names,
                                      abundance = abundances),
                   bin_type = "otu")
#> Assigned 3 otu bins.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 3 
#> Total number of seqs: 715 
#> 
#> Total number of otus: 3 
#> 

  strollur::count(data,
                    type = "bin",
                    bin_type = "otu")
#> [1] 3

  bins_to_remove <- c("bin1")
  trash_tag <- c("bad_bin")

  strollur::xdev_remove_bins(data,
                   bin_names = bins_to_remove,
                   trash_tags = trash_tag)
#> my_dataset:
#> 
#> 
#> scrap_summary:
#>       type trash_code unique total
#> 1 sequence    bad_bin      1   110
#> 2      otu    bad_bin      1   110
#> 
#> Number of unique seqs: 2 
#> Total number of seqs: 605 
#> 
#> Total number of otus: 2 
#> 

  strollur::count(data,
                    type = "bin",
                    bin_type = "otu")
#> [1] 2