statnmap/yatah

Yet Another TAxonomy Handler.

yatah

The goal of yatah is to manage taxonomy when lineages are described with strings and ranks separated with special patterns like |*__ or ;*__.

For instance, the well-known Escherichia coli could be coded as k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli.

Installation

You can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("abichat/yatah")

Example

library(yatah)

lineages <- c(
  "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Coriobacteriales",
  "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",
  "k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales",
  "k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales",
  "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",
  "k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales",
  "k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales",
  "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales",
  "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales"
)

• is_rank() checks if the lineages are of the desired rank.

is_rank(lineages, rank = "order")
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
is_rank(lineages, rank = "species")
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE

• is_clade() checks if the lineages belong to the desired clade.

is_clade(lineages, clade = "Proteobacteria", rank = "phylum")
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE

• last_clade() extracts the last clade of the lineages.

last_clade(lineages)
#> [1] "Coriobacteriales"  "Bacteroidales"     "Flavobacteriales" 
#> [4] "Bacillales"        "Lactobacillales"   "Clostridiales"    
#> [7] "Campylobacterales" "Enterobacteriales" "Pseudomonadales"

• all_clades extracts all clades of the lineages.

all_clades(lineages, simplify = TRUE)
#>  [1] "Actinobacteria"        "Actinobacteria"       
#>  [3] "Bacillales"            "Bacilli"              
#>  [5] "Bacteria"              "Bacteroidales"        
#>  [7] "Bacteroidetes"         "Bacteroidia"          
#>  [9] "Campylobacterales"     "Clostridia"           
#> [11] "Clostridiales"         "Coriobacteriales"     
#> [13] "Enterobacteriales"     "Epsilonproteobacteria"
#> [15] "Firmicutes"            "Flavobacteriales"     
#> [17] "Flavobacteriia"        "Gammaproteobacteria"  
#> [19] "Lactobacillales"       "Proteobacteria"       
#> [21] "Pseudomonadales"

• taxtable() computes the taxonomic table corresponding to the lineages.

table <- taxtable(lineages)
table
#>    kingdom         phylum                 class             order
#> 1 Bacteria Actinobacteria        Actinobacteria  Coriobacteriales
#> 2 Bacteria  Bacteroidetes           Bacteroidia     Bacteroidales
#> 3 Bacteria  Bacteroidetes        Flavobacteriia  Flavobacteriales
#> 4 Bacteria     Firmicutes               Bacilli        Bacillales
#> 5 Bacteria     Firmicutes               Bacilli   Lactobacillales
#> 6 Bacteria     Firmicutes            Clostridia     Clostridiales
#> 7 Bacteria Proteobacteria Epsilonproteobacteria Campylobacterales
#> 8 Bacteria Proteobacteria   Gammaproteobacteria Enterobacteriales
#> 9 Bacteria Proteobacteria   Gammaproteobacteria   Pseudomonadales

• taxtree() computes the taxonomic tree (format phylo) from a taxonomic table.

tree <- taxtree(table)
tree
#> 
#> Phylogenetic tree with 9 tips and 6 internal nodes.
#> 
#> Tip labels:
#>  Coriobacteriales, Bacteroidales, Flavobacteriales, Bacillales, Lactobacillales, Clostridiales, ...
#> Node labels:
#> [1] "Bacteria"            "Bacteroidetes"       "Firmicutes"         
#> [4] "Bacilli"             "Proteobacteria"      "Gammaproteobacteria"
#> 
#> Rooted; includes branch lengths.
plot(tree, show.node.label = TRUE)