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Extract Labels and Colors from Species Delimitation Partitions

Source: R/get_delim_cols.R
get_delim_cols.Rd

get_delim_cols() returns a tbl_df format containing extracted and processed data from delim_autoplot.

Usage

get_delim_cols(p, delimname = NULL, hap_tbl = NULL)

Arguments

p

Output from delim_autoplot.

delimname

A character vector of species delimitation names (optional). If provided, the function filters the data to only include rows matching such terms. Default to NULL.

hap_tbl

output from haplotype_tbl (optional). If provided, the function will annotate color and fill data for collapsed haplotypes. Default to NULL.

Value

an object of class tbl_df.

Details

get_delim_cols() is a convenience function to extract labels, species partitions, color and fill data from the output of delim_autoplot in a tbl_df format. It is best used when combined with haplotype information from haplotype_tbl or when combined with other metadata, such as GPS coordinates for map plotting.

Author

Pedro S. Bittencourt.

Examples


# plot using autoplot
p <- delim_autoplot(geophagus_delims, geophagus_beast)
#> Warning: ⚠ Argument `tbl_labs` not provided. Using tiplabels instead.
#> Warning: ⚠ Argument `delim_order` not provided. Using default order from
#> `geophagus_delims`.
#> Warning: ⚠ Argument `col_vec` not provided. Customizing one using `delim_brewer()`.
#> ℹ Please use `delimtools::delim_brewer()` to create even better colour
#>   palettes!
#> Warning: ⚠ `n_match` was not found. Using `n_match= 4` instead.

# view 
p


# get haplotypes
hap_tbl <- haplotype_tbl(geophagus)
#> Warning: ⚠ You have missing data "('N','-' '?')" or ambiguity inside your sequence, i.e.
#> not padding the ends, and this may have unintended consequences later, as they
#> have now been removed!
#> ℹ The names of the samples are bellow.
#> GU701784.1, GU701785.1

# extract colors for consensus
get_delim_cols(p, delimname= "consensus", hap_tbl= hap_tbl)
#> # A tibble: 354 × 6
#>    labels     method    spp   fill    colour  status   
#>    <chr>      <fct>     <fct> <chr>   <chr>   <chr>    
#>  1 MZ504432.1 consensus sp3   #C4625D #C4625D haplotype
#>  2 MZ504431.1 consensus sp3   #C4625D #C4625D haplotype
#>  3 MZ504433.1 consensus sp3   #C4625D #C4625D haplotype
#>  4 MZ504415.1 consensus sp3   #C4625D #C4625D haplotype
#>  5 MZ504442.1 consensus sp3   #C4625D #C4625D haplotype
#>  6 MZ504420.1 consensus sp3   #C4625D #C4625D haplotype
#>  7 MZ504424.1 consensus sp3   #C4625D #C4625D haplotype
#>  8 MZ504400.1 consensus sp3   #C4625D #C4625D haplotype
#>  9 MZ504414.1 consensus sp3   #C4625D #C4625D haplotype
#> 10 MZ504394.1 consensus sp3   #C4625D #C4625D haplotype
#> # ℹ 344 more rows