speedytax
The goal of speedytax is to quickly import classification files generated with the QIIME2 classifier, the RDP Classifier and the USEARCH or vsearch sintax classifier as phyloseq tax_table objects.
When importing RDP Classifier and sintax results, the confidence value can be specified on import. In the case of the QIIME2 classifier the confidence value must be given when calling the classifier.
All ranks are filled. If a taxa is unclassified at a given rank (i.e. the confidence value at that rank is less than that specified), “uncl_” is prepended to the classification at the higher rank and copied to all lower ranks.
For example, in the example below Hyphomicrobiales is classified to order and to uncl_Hyphomicrobiales at the family and genus levels.
Installation
You can install the development version of speedytax from GitHub with:
# install.packages("devtools")
devtools::install_github("jfq3/speedytax")You can install the latest release from CRAN with:
install.packages("speedytax")Example
This is an example of importing a classification file created with the RDP Classifier:
library(speedytax)
taxonomy_file <- read_tax_example("rdp_table.tsv")
example_tax_table <- import_rdp_tax_table(in_file = taxonomy_file)
example_tax_table
#> Taxonomy Table: [10 taxa by 6 taxonomic ranks]:
#> Domain Phylum
#> 15dac1e6a414861c0db80d636ffb8a9a "Bacteria" "Acidobacteriota"
#> 58738b7c9e86d0e83a8c3f33c6778e93 "Bacteria" "Pseudomonadota"
#> 714b0378efe0b8744e24aa04b48008d3 "Bacteria" "Bacillota"
#> 72d78ad803e3cfc73fca6825e5fcddc1 "Bacteria" "Nitrospirota"
#> 8cb24777cb48dde0aac60dfeca125d10 "Bacteria" "Bacillota"
#> 8d2a29d23de2d1b6cada06bf85915274 "Bacteria" "Pseudomonadota"
#> 9db2817f5c42be6a7bcbca662959982d "Bacteria" "Pseudomonadota"
#> ad5db97e5236e5b1b1e5728586c8e087 "Bacteria" "Pseudomonadota"
#> dc01606f995091a4a41ad216f02a265b "Bacteria" "Cyanobacteriota"
#> fb75fa1fac5ad54c9d64c653e50a7126 "Bacteria" "Pseudomonadota"
#> Class Order
#> 15dac1e6a414861c0db80d636ffb8a9a "Acidobacteria_Gp16" "Gp16"
#> 58738b7c9e86d0e83a8c3f33c6778e93 "Alphaproteobacteria" "Sphingomonadales"
#> 714b0378efe0b8744e24aa04b48008d3 "Bacilli" "Caryophanales"
#> 72d78ad803e3cfc73fca6825e5fcddc1 "Nitrospiria" "Nitrospirales"
#> 8cb24777cb48dde0aac60dfeca125d10 "Bacilli" "Caryophanales"
#> 8d2a29d23de2d1b6cada06bf85915274 "Alphaproteobacteria" "Sphingomonadales"
#> 9db2817f5c42be6a7bcbca662959982d "Alphaproteobacteria" "Hyphomicrobiales"
#> ad5db97e5236e5b1b1e5728586c8e087 "Alphaproteobacteria" "Hyphomicrobiales"
#> dc01606f995091a4a41ad216f02a265b "Cyanophyceae" "Coleofasciculales"
#> fb75fa1fac5ad54c9d64c653e50a7126 "Alphaproteobacteria" "Hyphomicrobiales"
#> Family
#> 15dac1e6a414861c0db80d636ffb8a9a "Gp16"
#> 58738b7c9e86d0e83a8c3f33c6778e93 "Sphingomonadaceae"
#> 714b0378efe0b8744e24aa04b48008d3 "Bacillaceae"
#> 72d78ad803e3cfc73fca6825e5fcddc1 "Nitrospiraceae"
#> 8cb24777cb48dde0aac60dfeca125d10 "Bacillaceae"
#> 8d2a29d23de2d1b6cada06bf85915274 "Sphingomonadaceae"
#> 9db2817f5c42be6a7bcbca662959982d "Bradyrhizobiaceae"
#> ad5db97e5236e5b1b1e5728586c8e087 "uncl_Hyphomicrobiales"
#> dc01606f995091a4a41ad216f02a265b "Wilmottiaceae"
#> fb75fa1fac5ad54c9d64c653e50a7126 "Bradyrhizobiaceae"
#> Genus
#> 15dac1e6a414861c0db80d636ffb8a9a "Gp16"
#> 58738b7c9e86d0e83a8c3f33c6778e93 "Sphingomonas"
#> 714b0378efe0b8744e24aa04b48008d3 "Priestia"
#> 72d78ad803e3cfc73fca6825e5fcddc1 "Nitrospira"
#> 8cb24777cb48dde0aac60dfeca125d10 "Bacillus"
#> 8d2a29d23de2d1b6cada06bf85915274 "Sphingomonas"
#> 9db2817f5c42be6a7bcbca662959982d "Bradyrhizobium"
#> ad5db97e5236e5b1b1e5728586c8e087 "uncl_Hyphomicrobiales"
#> dc01606f995091a4a41ad216f02a265b "Pycnacronema"
#> fb75fa1fac5ad54c9d64c653e50a7126 "Bradyrhizobium"