P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-24 10:16:23 +02:00
Code Releases Activity

(v3.0.1.9059) Update taxonomy of microorganisms

Browse Source
This commit is contained in:
Matthijs Berends
2026-06-23 01:38:13 +02:00
committed by GitHub
parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
R/custom_microorganisms.R
View File

@@ -195,11 +195,13 @@ add_custom_microorganisms <- function(x) {
if (!"fullname" %in% colnames(x)) {
x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies))
}
if (!"domain" %in% colnames(x)) x$domain <- ""
if (!"kingdom" %in% colnames(x)) x$kingdom <- ""
if (!"phylum" %in% colnames(x)) x$phylum <- ""
if (!"class" %in% colnames(x)) x$class <- ""
if (!"order" %in% colnames(x)) x$order <- ""
if (!"family" %in% colnames(x)) x$family <- ""
x$domain[is.na(x$domain)] <- ""
x$kingdom[is.na(x$kingdom)] <- ""
x$phylum[is.na(x$phylum)] <- ""
x$class[is.na(x$class)] <- ""
@@ -217,6 +219,7 @@ add_custom_microorganisms <- function(x) {
# fill in taxonomy based on genus
genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE)
x$domain[which(x$domain == "" & genus_to_check != "")] <- AMR_env$MO_lookup$domain[match(genus_to_check[which(x$domain == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
x$kingdom[which(x$kingdom == "" & genus_to_check != "")] <- AMR_env$MO_lookup$kingdom[match(genus_to_check[which(x$kingdom == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
x$phylum[which(x$phylum == "" & genus_to_check != "")] <- AMR_env$MO_lookup$phylum[match(genus_to_check[which(x$phylum == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
x$class[which(x$class == "" & genus_to_check != "")] <- AMR_env$MO_lookup$class[match(genus_to_check[which(x$class == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
@@ -229,9 +232,9 @@ add_custom_microorganisms <- function(x) {
x$prevalence[is.na(x$prevalence)] <- 1.25
x$status <- "accepted"
x$ref <- paste("Self-added,", format(Sys.Date(), "%Y"))
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
# complete missing kingdom index, so mo_matching_score() will not return NA
x$kingdom_index[is.na(x$kingdom_index)] <- 1
x$domain_index <- AMR_env$MO_lookup$domain_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
# complete missing domain index, so mo_matching_score() will not return NA
x$domain_index[is.na(x$domain_index)] <- 1
x$fullname_lower <- tolower(x$fullname)
x$full_first <- substr(x$fullname_lower, 1, 1)
x$species_first <- tolower(substr(x$species, 1, 1))