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(v0.8.0.9007) Enterobacterales order

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dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
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91
data-raw/reproduction_of_microorganisms.R
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@ -663,6 +663,97 @@ MOs <- MOs %>%
species_id = ""),
)
# Incorporate new microbial order for Gammaproteobacteria - Adeolu et al. (2016), PMID 27620848
MOs[which(MOs$family == "Enterobacteriaceae"), "family"] <- ""
MOs[which(MOs$genus %in% c("Escherichia",
"Atlantibacter",
"Biostraticola",
"Buttiauxella",
"Cedecea",
"Citrobacter",
"Cronobacter",
"Enterobacillus",
"Enterobacter",
"Franconibacter",
"Gibbsiella",
"Izhakiella",
"Klebsiella",
"Kluyvera",
"Kosakonia",
"Leclercia",
"Lelliottia",
"Mangrovibacter",
"Pluralibacter",
"Pseudocitrobacter",
"Raoultella",
"Rosenbergiella",
"Saccharobacter",
"Salmonella",
"Shigella",
"Shimwellia",
"Siccibacter",
"Trabulsiella",
"Yokenella")), "family"] <- "Enterobacteriaceae"
MOs[which(MOs$genus %in% c("Erwinia",
"Buchnera",
"Pantoea",
"Phaseolibacter",
"Tatumella",
"Wigglesworthia")), "family"] <- "Erwiniaceae"
MOs[which(MOs$genus %in% c("Pectobacterium",
"Brenneria",
"Dickeya",
"Lonsdalea",
"Sodalis")), "family"] <- "Pectobacteriaceae"
MOs[which(MOs$genus %in% c("Yersinia",
"Chania",
"Ewingella",
"Rahnella",
"Rouxiella",
"Samsonia",
"Serratia")), "family"] <- "Yersiniaceae"
MOs[which(MOs$genus %in% c("Hafnia",
"Edwardsiella",
"Obesumbacterium")), "family"] <- "Hafniaceae"
MOs[which(MOs$genus %in% c("Morganella",
"Arsenophonus",
"Cosenzaea",
"Moellerella",
"Photorhabdus",
"Proteus",
"Providencia",
"Xenorhabdus")), "family"] <- "Morganellaceae"
MOs[which(MOs$genus %in% c("Budvicia",
"Leminorella",
"Pragia")), "family"] <- "Budviciaceae"
MOs[which(MOs$family %in% c("Enterobacteriaceae",
"Erwiniaceae",
"Pectobacteriaceae",
"Yersiniaceae",
"Hafniaceae",
"Morganellaceae",
"Budviciaceae")), "order"] <- "Enterobacterales"
new_families <- MOs %>%
filter(order == "Enterobacterales") %>%
pull(family) %>%
unique()
class(MOs$mo) <- "character"
MOs <- rbind(MOs %>% filter(!(rank == "family" & fullname %in% new_families)),
AMR::microorganisms %>%
filter(family == "Enterobacteriaceae" & rank == "family") %>%
rbind(., ., ., ., ., ., .) %>%
mutate(fullname = new_families,
source = "manually added",
ref = "Adeolu et al., 2016",
family = fullname, mo = paste0("B_[FAM]_",
toupper(abbreviate(new_families,
minlength = 8,
use.classes = TRUE,
method = "both.sides",
strict = FALSE)))))
MOs[which(MOs$order == "Enterobacteriales"), "order"] <- "Enterobacterales"
MOs[which(MOs$fullname == "Enterobacteriales"), "fullname"] <- "Enterobacterales"
MOs <- MOs %>%
group_by(kingdom) %>%
distinct(fullname, .keep_all = TRUE) %>%