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.
You can install the released version of yatah from CRAN with:
install.packages("yatah")And the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("abichat/yatah")library(yatah)yatah handles 8 different ranks:
all_ranks
#> [1] "kingdom" "phylum" "class" "order" "family" "genus" "species" "strain"A lineage is composed of a succession of clades separated by special characters indicating the current rank.
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"
)yatah offers functions to verify if lineages meet a desired property, to extract information, or to compute summary objects.
is_rank() and is_at_least_rank() check if
the lineages are of the desired rank.is_rank(lineages, rank = "order")
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
is_at_least_rank(lineages, rank = "species")
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSEis_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 TRUEget_clade() extracts the clade of the desired
rank.get_clade(lineages, rank = "class")
#> [1] "Actinobacteria" "Bacteroidia" "Flavobacteriia" "Bacilli"
#> [5] "Bacilli" "Clostridia" "Epsilonproteobacteria" "Gammaproteobacteria"
#> [9] "Gammaproteobacteria"get_last_clade() extracts the last clade of the
lineages.get_last_clade(lineages)
#> [1] "Coriobacteriales" "Bacteroidales" "Flavobacteriales" "Bacillales" "Lactobacillales"
#> [6] "Clostridiales" "Campylobacterales" "Enterobacteriales" "Pseudomonadales"get_all_clades() extracts all clades of the
lineages.get_all_clades(lineages, simplify = TRUE)
#> [1] "Actinobacteria" "Bacillales" "Bacilli" "Bacteria"
#> [5] "Bacteroidales" "Bacteroidetes" "Bacteroidia" "Campylobacterales"
#> [9] "Clostridia" "Clostridiales" "Coriobacteriales" "Enterobacteriales"
#> [13] "Epsilonproteobacteria" "Firmicutes" "Flavobacteriales" "Flavobacteriia"
#> [17] "Gammaproteobacteria" "Lactobacillales" "Proteobacteria" "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 Pseudomonadalestaxtree() 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:
#> Bacteria, Bacteroidetes, Firmicutes, Bacilli, Proteobacteria, Gammaproteobacteria
#>
#> Rooted; includes branch lengths.
plot(tree, show.node.label = TRUE)
If you want to change the default separator from | to,
e.g., ;, use options(yatah_sep = ";"). Reset
it with options(yatah_sep = "\\|").