mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 16:22:10 +02:00
sort sir history
This commit is contained in:
@ -32,26 +32,26 @@
|
||||
#' With [add_custom_microorganisms()] you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
|
||||
#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing column "genus" (case-insensitive)
|
||||
#' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
|
||||
#'
|
||||
#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
|
||||
#'
|
||||
#'
|
||||
#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
|
||||
#'
|
||||
#' There are two ways to automate this process:
|
||||
#'
|
||||
#'
|
||||
#' **Method 1:** Using the option [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
|
||||
#'
|
||||
#'
|
||||
#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
|
||||
#'
|
||||
#'
|
||||
#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
|
||||
#'
|
||||
#' ```r
|
||||
#' # Add custom microorganism codes:
|
||||
#' options(AMR_custom_mo = "~/my_custom_mo.rds")
|
||||
#' ```
|
||||
#'
|
||||
#'
|
||||
#' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function.
|
||||
#'
|
||||
#'
|
||||
#' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method:
|
||||
#'
|
||||
#'
|
||||
#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
|
||||
#'
|
||||
#' 2. Add a text like below and save the file:
|
||||
@ -77,44 +77,49 @@
|
||||
#' # now add a custom entry - it will be considered by as.mo() and
|
||||
#' # all mo_*() functions
|
||||
#' add_custom_microorganisms(
|
||||
#' data.frame(genus = "Enterobacter",
|
||||
#' species = "asburiae/cloacae"
|
||||
#' data.frame(
|
||||
#' genus = "Enterobacter",
|
||||
#' species = "asburiae/cloacae"
|
||||
#' )
|
||||
#' )
|
||||
#'
|
||||
#' # E. asburiae/cloacae is now a new microorganism:
|
||||
#' mo_name("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#'
|
||||
#' # its code:
|
||||
#' as.mo("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#'
|
||||
#' # all internal algorithms will work as well:
|
||||
#' mo_name("Ent asburia cloacae")
|
||||
#'
|
||||
#'
|
||||
#' # and even the taxonomy was added based on the genus!
|
||||
#' mo_family("E. asburiae/cloacae")
|
||||
#' mo_gramstain("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#' mo_info("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#'
|
||||
#'
|
||||
#'
|
||||
#' # the function tries to be forgiving:
|
||||
#' add_custom_microorganisms(
|
||||
#' data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
|
||||
#' SPECIES = "SPECIES")
|
||||
#' data.frame(
|
||||
#' GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
|
||||
#' SPECIES = "SPECIES"
|
||||
#' )
|
||||
#' )
|
||||
#' mo_name("BACTEROIDES / PARABACTEROIDES")
|
||||
#' mo_rank("BACTEROIDES / PARABACTEROIDES")
|
||||
#'
|
||||
#'
|
||||
#' # taxonomy still works, although a slashline genus was given as input:
|
||||
#' mo_family("Bacteroides/Parabacteroides")
|
||||
#'
|
||||
#'
|
||||
#'
|
||||
#'
|
||||
#' # for groups and complexes, set them as species or subspecies:
|
||||
#' add_custom_microorganisms(
|
||||
#' data.frame(genus = "Citrobacter",
|
||||
#' species = c("freundii", "braakii complex"),
|
||||
#' subspecies = c("complex", ""))
|
||||
#' data.frame(
|
||||
#' genus = "Citrobacter",
|
||||
#' species = c("freundii", "braakii complex"),
|
||||
#' subspecies = c("complex", "")
|
||||
#' )
|
||||
#' )
|
||||
#' mo_name(c("C. freundii complex", "C. braakii complex"))
|
||||
#' mo_species(c("C. freundii complex", "C. braakii complex"))
|
||||
@ -123,9 +128,9 @@
|
||||
add_custom_microorganisms <- function(x) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
|
||||
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
|
||||
# remove any extra class/type, such as grouped tbl, or data.table:
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- tolower(colnames(x))
|
||||
@ -135,7 +140,7 @@ add_custom_microorganisms <- function(x) {
|
||||
}
|
||||
# keep only columns available in the microorganisms data set
|
||||
x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE]
|
||||
|
||||
|
||||
# clean the input ----
|
||||
for (col in c("genus", "species", "subspecies")) {
|
||||
if (!col %in% colnames(x)) {
|
||||
@ -152,7 +157,7 @@ add_custom_microorganisms <- function(x) {
|
||||
col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
|
||||
# groups are in our taxonomic table with a capital G
|
||||
col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
|
||||
|
||||
|
||||
col_[is.na(col_)] <- ""
|
||||
if (col == "genus") {
|
||||
substr(col_, 1, 1) <- toupper(substr(col_, 1, 1))
|
||||
@ -163,19 +168,27 @@ add_custom_microorganisms <- function(x) {
|
||||
x[, col] <- col_
|
||||
}
|
||||
# if subspecies is a group or complex, add it to the species and empty the subspecies
|
||||
x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
|
||||
x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))])
|
||||
x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(
|
||||
x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
|
||||
x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))]
|
||||
)
|
||||
x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))] <- ""
|
||||
|
||||
|
||||
if ("rank" %in% colnames(x)) {
|
||||
stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),
|
||||
"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank))
|
||||
stop_ifnot(
|
||||
all(x$rank %in% AMR_env$MO_lookup$rank),
|
||||
"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank)
|
||||
)
|
||||
} else {
|
||||
x$rank <- ifelse(x$subspecies != "", "subspecies",
|
||||
ifelse(x$species != "", "species",
|
||||
ifelse(x$genus != "", "genus",
|
||||
stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
|
||||
call. = FALSE))))
|
||||
ifelse(x$species != "", "species",
|
||||
ifelse(x$genus != "", "genus",
|
||||
stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
|
||||
call. = FALSE
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
}
|
||||
x$source <- "Added by user"
|
||||
if (!"fullname" %in% colnames(x)) {
|
||||
@ -191,7 +204,7 @@ add_custom_microorganisms <- function(x) {
|
||||
x$class[is.na(x$class)] <- ""
|
||||
x$order[is.na(x$order)] <- ""
|
||||
x$family[is.na(x$family)] <- ""
|
||||
|
||||
|
||||
for (col in colnames(x)) {
|
||||
if (is.factor(x[, col, drop = TRUE])) {
|
||||
x[, col] <- as.character(x[, col, drop = TRUE])
|
||||
@ -200,7 +213,7 @@ add_custom_microorganisms <- function(x) {
|
||||
x[, col] <- as.list(x[, col, drop = TRUE])
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
# fill in taxonomy based on genus
|
||||
genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE)
|
||||
x$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)]
|
||||
@ -208,7 +221,7 @@ add_custom_microorganisms <- function(x) {
|
||||
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$genus)]
|
||||
x$order[which(x$order == "" & genus_to_check != "")] <- AMR_env$MO_lookup$order[match(genus_to_check[which(x$order == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
|
||||
|
||||
# fill in other columns that are used in internal algorithms
|
||||
x$prevalence <- NA_real_
|
||||
x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
@ -222,7 +235,7 @@ add_custom_microorganisms <- function(x) {
|
||||
x$full_first <- substr(x$fullname_lower, 1, 1)
|
||||
x$species_first <- tolower(substr(x$species, 1, 1))
|
||||
x$subspecies_first <- tolower(substr(x$subspecies, 1, 1))
|
||||
|
||||
|
||||
if (!"mo" %in% colnames(x)) {
|
||||
# create the mo code
|
||||
x$mo <- NA_character_
|
||||
@ -230,19 +243,27 @@ add_custom_microorganisms <- function(x) {
|
||||
x$mo <- trimws2(as.character(x$mo))
|
||||
x$mo[x$mo == ""] <- NA_character_
|
||||
current <- sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE)
|
||||
x$mo[is.na(x$mo)] <- paste0("CUSTOM",
|
||||
seq.int(from = current + 1, to = current + nrow(x), by = 1),
|
||||
"_",
|
||||
toupper(unname(abbreviate(gsub(" +", " _ ",
|
||||
gsub("[^A-Za-z0-9-]", " ",
|
||||
trimws2(paste(x$genus, x$species, x$subspecies)))),
|
||||
minlength = 10))))
|
||||
x$mo[is.na(x$mo)] <- paste0(
|
||||
"CUSTOM",
|
||||
seq.int(from = current + 1, to = current + nrow(x), by = 1),
|
||||
"_",
|
||||
toupper(unname(abbreviate(
|
||||
gsub(
|
||||
" +", " _ ",
|
||||
gsub(
|
||||
"[^A-Za-z0-9-]", " ",
|
||||
trimws2(paste(x$genus, x$species, x$subspecies))
|
||||
)
|
||||
),
|
||||
minlength = 10
|
||||
)))
|
||||
)
|
||||
stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
|
||||
|
||||
|
||||
# add to package ----
|
||||
AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
|
||||
class(AMR_env$MO_lookup$mo) <- "character"
|
||||
|
||||
|
||||
new_df <- AMR_env$MO_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
|
||||
rownames(new_df) <- NULL
|
||||
list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
|
||||
@ -254,10 +275,10 @@ add_custom_microorganisms <- function(x) {
|
||||
# assign new values
|
||||
new_df[, col] <- x[, col, drop = TRUE]
|
||||
}
|
||||
|
||||
|
||||
# clear previous coercions
|
||||
suppressMessages(mo_reset_session())
|
||||
|
||||
|
||||
AMR_env$MO_lookup <- unique(rbind(AMR_env$MO_lookup, new_df))
|
||||
class(AMR_env$MO_lookup$mo) <- c("mo", "character")
|
||||
if (nrow(x) <= 3) {
|
||||
@ -271,11 +292,11 @@ add_custom_microorganisms <- function(x) {
|
||||
#' @export
|
||||
clear_custom_microorganisms <- function() {
|
||||
n <- nrow(AMR_env$MO_lookup)
|
||||
|
||||
|
||||
# reset
|
||||
AMR_env$MO_lookup <- NULL
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
|
||||
n2 <- nrow(AMR_env$MO_lookup)
|
||||
AMR_env$custom_mo_codes <- character(0)
|
||||
AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
|
||||
|
||||
Reference in New Issue
Block a user